I have also experienced this, with both OOTP5 and OOTP6. Never saw it on the boards - figured maybe it was my mouse. But it only happened in the Player Tracker screen. It was as if both the "down click" and "up click" of a single mouse click were each registering as single mouse clicks, so one "down-up" click would actually delete two players from the Player Tracker. It's nearly impossible for me to get it to only delete one. I usually try to delete two at a time and sort the list so that I can get the two I want to drop next to each other.
It's nice to know it isn't just me.