I actually think I know this one.
Say a Pokémon you're training levels up mid battle, and it gains the +2 or whatever to its Max HP. If that Pokémon was at, lets say, 75/100 HP, it would then change to 75/102HP.
I think the same thing may be happening as the EVs increase your idle Pokémon's HP stat. It will be at full health, then minus whatever health it gains from the EV boost.
I think...