MacOS encodes characters (in filenames) in decomposed form (NFD), while everyone else uses the composed form (NFC). When adding filenames using Git the decomposed form enters the repository, since Git (except on Windows) does not recode the filenames it reads from disk.
EGit assumes the composed form is used. If you use non-ascii names on Mac, only use EGit or JGit with the repo, unless you are aware of the issues.
Git for Windows as of 1.7.10 uses UTF-8 NFC.
Composed for means that a character like "Ä" is encoded as one unicode character, while the decomposed form means it is encoded as "A" + "Add two dots above previous character".
$ touch Ä
$ echo Ä|od -tx1a
0000000    c3  84  0a                                                    
           ?  84  nl                                                    
0000003
$ ls|od -tx1a
0000000    41  cc  88  0a                                                
           A   ?  88  nl                                                
0000004
$ 
Update: Since 1.7.12 native git on OS X has an option to precompose non-ASCII characters in a way that is compatible with both EGit and Git on Windows. You need to configure core.precomposeunicode to true.