There seems to be a problem with games where one player passes and the other plays on. Not only the move numbering is weird but if you have uploaded an .sgf like this things will be broken. See for example https://online-go.com/game/2673533
I edited it to show how capturing no longer works after pass:
The “capture not working” part is desired behavior, Meepy.
Hold on a second, I can hear you gasping: in truth it is about the difference between making a move and placing/editing stones (that difference should be clear when you change from “alternating” to all black or all white).
Now the real problem here is that not handling passes properly makes the system go bonkers and think they are editing the same position instead of playing.
It really is a serious issue, though it may not seem so, thanks for bringing this up. I hope it gets addressed soon enough. Have you considered submitting it to uservoice?