Any program running on any non-realtime OS can stop for any number of milliseconds. There are a billion reasons for such interruptions like other processes wanting to run, cleanup phases internal to the OS, memory paging...
If your program stops for 50 ms, do you really care if it was because of a GC cycle or something else? If you really do care, then you are not allowed to target Linux, Windows or OS X all of which are decidedly not real time operating systems.