I do not exactly know when this happens, but sometimes there are weird breakpoints that are automatically added on the very first line of (it seems) every loaded source file. I did not notice this bug before version 0.3.9.5
I'm experiencing a version of this (using 0.3.9.6.):
Sometimes when setting a breakpoint, some other lines in the code base also semi-randomly get one, and it would also break at one of those places directly (not where I wanted to break originally).
"Semi-randomly" because it seems to reoccur for certain lines, but not affect wildly different ones over time.
Might have started noticing it in 0.3.9.5 or so. Not sure.