I'm no expert by any means. but last week I was cutting straight lines on a sheet of mdf. I drew a box instead of straight lines so that it wouldn't do a line then travel back to start the next wasting travel time. I went out side the sheet so it didn't cut on the ends of the box. problem was that I used another box to align the other boxes. when I went to remove the alignment box I cut it instead of deleting it. I ended up with multiple lines on top of each other in one spot.
this created tool paths on those lines and it was cut twice . a bit wasteful. probably 30 seconds on a 15 min cut but no big deal.

it sounds like you have a similar issue. something isn't joined up fully or has hidden lines