Effectivement, avec le dernier code posté (le mien en l'occurence) la matrice ne présente pas de NaN. Nous avons donc un écart de code avec toi.
La seul remarque que je peux faire, c'est que cette matrice est carrée et non plus n*m comme indiqué par

           final int NB_POINTS = 9;
	   private int n = NB_POINTS;

	   private int m = NB_POINTS - 1;

	   // Matrice des positions initiales
	   public double[][] coordonneesInitiales = new double[n][m];

La définition de m n'est peut-être pas bonne dans ton algorithme.

Résultat avec m=NB_POINTS - 1

Matrice Initiale Complète
0|   0.099   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
1|   0.065   0.292   0.0   0.0   0.0   0.0   0.0   0.0   
2|   0.478   0.612   0.059   0.0   0.0   0.0   0.0   0.0   
3|   0.748   0.791   0.885   0.244   0.0   0.0   0.0   0.0   
4|   0.35   0.306   0.032   0.114   0.367   0.0   0.0   0.0   
5|   0.132   0.077   0.876   0.079   0.15   0.87   0.0   0.0   
6|   0.963   0.061   0.335   0.75   0.966   0.878   0.998   0.0   
7|   0.166   0.547   0.288   0.3   0.759   0.557   0.919   0.756   
8|   0.017   0.842   0.067   0.895   0.68   0.137   0.921   0.91   
Matrice distance
0|   0.0   0.2939727878562912   0.7222644944893802   1.374642862710166   0.552581215750228   1.24901361081455   2.0310061545943183   1.6670539883279125   
1|   0.2939727878562912   0.0   0.5257851272145304   1.2482992429702104   0.47971866755422393   1.266385012545553   2.057798338030236   1.5970588592785178   
2|   0.7222644944893802   0.5257851272145304   0.0   0.9201918278272201   0.5083640427882365   1.363477539235612   1.969148546961351   1.595755933719189   
3|   1.374642862710166   1.2482992429702104   0.9201918278272201   0.0   1.1281963481593087   1.3022895223413264   1.9590061255646956   1.749351879982984   
4|   0.552581215750228   0.47971866755422393   0.5083640427882365   1.1281963481593087   0.0   1.2718156312925235   1.7486531960340221   1.4394717781186266   
5|   1.24901361081455   1.266385012545553   1.363477539235612   1.3022895223413264   1.2718156312925235   0.0   1.759449629855882   1.581640920057394   
6|   2.0310061545943183   2.057798338030236   1.969148546961351   1.9590061255646956   1.7486531960340221   1.759449629855882   0.0   1.3415591675360428   
7|   1.6670539883279125   1.5970588592785178   1.595755933719189   1.749351879982984   1.4394717781186266   1.581640920057394   1.3415591675360428   0.0   
8|   1.9179968717388463   1.807713472871185   1.79555562431243   1.9461235829206738   1.674051970519434   2.1007896134549027   1.7500377138793324   0.8476160687481095   
Matrice resultat
0|   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
1|   0.2939727878562912   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
2|   0.5640590110709848   0.4511135467148184   0.0   0.0   0.0   0.0   0.0   0.0   
3|   0.7106304006006282   0.845553235494761   0.8183441572385862   0.0   0.0   0.0   0.0   0.0   
4|   0.2749166022792148   0.28644631519585045   0.02873032815495471   0.38326223208931004   0.0   0.0   0.0   0.0   
5|   0.07266658984246778   0.15589590626950392   0.8473239749681973   0.09120659782029286   0.8967577549635228   0.0   0.0   0.0   
6|   -0.039336974297272766   0.9016385736644148   0.43262071765637694   1.1125176690221803   0.768253031155888   1.138164098810563   0.0   0.0   
7|   0.5355801846426934   0.1663664752428089   0.34578205869891643   0.7862465808992009   0.5455242010622685   0.8608568453856572   0.829532989969456   0.0   
8|   0.8458333909516604   0.02455934664270381   0.3282700085960744   0.8918283358684781   -0.013458714498495766   1.1051221730801026   0.7882142842439311   0.4656155299457704   
Nombre NaN :0.0

Résultat avec m=NB_POINTS

Matrice Initiale Complète
0|   0.099   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
1|   0.065   0.292   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
2|   0.478   0.612   0.059   0.0   0.0   0.0   0.0   0.0   0.0   
3|   0.748   0.791   0.885   0.244   0.0   0.0   0.0   0.0   0.0   
4|   0.35   0.306   0.032   0.114   0.367   0.0   0.0   0.0   0.0   
5|   0.132   0.077   0.876   0.079   0.15   0.87   0.0   0.0   0.0   
6|   0.963   0.061   0.335   0.75   0.966   0.878   0.998   0.0   0.0   
7|   0.166   0.547   0.288   0.3   0.759   0.557   0.919   0.756   0.0   
8|   0.017   0.842   0.067   0.895   0.68   0.137   0.921   0.91   0.547   
Matrice distance
0|   0.0   0.2939727878562912   0.7222644944893802   1.374642862710166   0.552581215750228   1.24901361081455   2.0310061545943183   1.6670539883279125   1.9944726119954619   
1|   0.2939727878562912   0.0   0.5257851272145304   1.2482992429702104   0.47971866755422393   1.266385012545553   2.057798338030236   1.5970588592785178   1.8886601070600288   
2|   0.7222644944893802   0.5257851272145304   0.0   0.9201918278272201   0.5083640427882365   1.363477539235612   1.969148546961351   1.595755933719189   1.8770266380635094   
3|   1.374642862710166   1.2482992429702104   0.9201918278272201   0.0   1.1281963481593087   1.3022895223413264   1.9590061255646956   1.749351879982984   2.0215355549680547   
4|   0.552581215750228   0.47971866755422393   0.5083640427882365   1.1281963481593087   0.0   1.2718156312925235   1.7486531960340221   1.4394717781186266   1.7611527474923918   
5|   1.24901361081455   1.266385012545553   1.363477539235612   1.3022895223413264   1.2718156312925235   0.0   1.759449629855882   1.581640920057394   2.170835323095697   
6|   2.0310061545943183   2.057798338030236   1.969148546961351   1.9590061255646956   1.7486531960340221   1.759449629855882   0.0   1.3415591675360428   1.833532383133715   
7|   1.6670539883279125   1.5970588592785178   1.595755933719189   1.749351879982984   1.4394717781186266   1.581640920057394   1.3415591675360428   0.0   1.0087923473143519   
8|   1.9944726119954619   1.8886601070600288   1.8770266380635094   2.0215355549680547   1.7611527474923918   2.170835323095697   1.833532383133715   1.0087923473143519   0.0   
Matrice resultat
0|   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
1|   0.2939727878562912   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
2|   0.5640590110709848   0.4511135467148184   0.0   0.0   0.0   0.0   0.0   0.0   0.0   
3|   0.7106304006006282   0.845553235494761   0.8183441572385862   0.0   0.0   0.0   0.0   0.0   0.0   
4|   0.2749166022792148   0.28644631519585045   0.02873032815495471   0.38326223208931004   0.0   0.0   0.0   0.0   0.0   
5|   0.07266658984246778   0.15589590626950392   0.8473239749681973   0.09120659782029286   0.8967577549635228   0.0   0.0   0.0   0.0   
6|   -0.039336974297272766   0.9016385736644148   0.43262071765637694   1.1125176690221803   0.768253031155888   1.138164098810563   0.0   0.0   0.0   
7|   0.5355801846426934   0.1663664752428089   0.34578205869891643   0.7862465808992009   0.5455242010622685   0.8608568453856572   0.829532989969456   0.0   0.0   
8|   0.8458333909516619   0.024559346642701103   0.3282700085960759   0.8918283358684784   -0.013458714498497065   1.105122173080105   0.7882142842439279   0.7183361481414366   0.0   
Nombre NaN :0.0

Le parcours dans le 2ème cas est complet pour la matrice, ce qui n'est pas le cas dans m=n-1