On the whole defMON is a fairly stable program, but there are a bunch of glitches here and there. If you find reproducible bugs yourself, don't hesitate to add them here. Please specify which version of the program you are talking about!
The SHIFT + U function (create a new sequence at the next unused slot) does not work correctly in stereo sid mode. It only scans for unused sequences in the sequence list for SID #1, so if you use it in the SID #2 sequence list, it might wrongly assume that a sequence is unused just because it isn't used for SID #2, and then this sequence will be overwritten.
Channel muting on the second sid does not work in 2014-06-15. Pressing F7 to stop the music doesn't make the second SID go silent either.
Packing as raw does not work in 2014-06-15. The option to name the file doesn't come up.
If you have more files on a disk side than what fits on the screen in the disk menu, RAM will be overwritten and corrupted. Watch out!