During the season. If you keep a player on the 40-Man and put them on Waivers, you can then remove the player from Waivers if he's claimed or remove him from the 40-Man if he clears.
The easiest way to get rid of this is to disable the item from the menus if the setting "Allow waiver trades after the deadline" is unchecked.
Another issue in the game is ability to DFA players who aren't on the 40-Man. The AI won't make such moves but human GMs can move players from a minor league roster to DFA to get around roster limits.
Although MLB teams might not typically claim a player on Unconditional Release Waivers (see below) it can happen.
From MLB.com:
https://www.mlb.com/glossary/transac...elease-waivers
Quote:
Before a club can formally release a player, that player must first be passed through unconditional release waivers. All 29 other clubs in the Majors have the opportunity to claim the player and add him to their 40-man rosters. A player that is claimed on release waivers has the option of rejecting that claim and instead exploring the free-agent market.
Release waivers are often requested after a player's contract is designated for assignment or in cases when a veteran player would otherwise refuse an outright assignment. Players are rarely claimed off release waivers, as the claiming club is required to pick up the remaining contract. Once the player clears waivers, the releasing club is responsible for the old contract.
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Right now, I can release a player directly and avoid waivers. This last part isn't a big deal because, as you say, it rarely happens but there are situations where GMs can get a chance to resign the player to a cheaper contract rather than have an opponent win a waiver claim. (It's happened in my online league before.)