In my draft-pick negotiation page, I have a player, Sean Bouchard, who appears twice. I submitted this offer to only one of him, but it automatically appeared in both places that he is listed. I also checked my team's finances after offering him, and the "offered contracts" expense section was listed at $620,000 (so twice the $310,000 I offered him). Another thing is that while it says that he was drafted in the 3rd round, 90th overall for both of his listings, I could have sworn that one of them was listed a 2nd round pick before I offered him. I'm relatively new to the game, and I'm using this league just to test the waters, so I just went with my scouting director's recommendation for all of my picks. I say this because it's possible that he was actually in the player pool twice and I drafted him twice without noticing.
EDIT: I just checked the draft log, and he was indeed drafted twice. 2nd round 19th pick and 3rd round 20th pick.
EDIT #2: He accepted the $310,000 offer and now only appears once on the minor league team he was assigned to. The bonus was only expensed once in my draft expenses so both of those things are okay. So I guess the only problem now is the fact that I was able to draft a player after I had just drafted him in the previous round.
Some other things worth noting:
1) I didn't realize until after the draft pool was announced that I didn't have enough feeder teams to fill the draft, resulting in some new players being generated for the pool.
2) In my league rules page, I set the draft rounds to 50, and set it to generate players for I think 55 rounds. However, the game automatically set the draft to 90 rounds somewhere along the way, and I had to change it back manually right before I started the draft.