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This typically happens when the growth curve of a Pokemon and its evolution are different. A Pokemon's level is essentially just a formula of how many levels their current exp would get them in their level up group. If a Pokemon evolves into a different group it will recalculate and may find itself at a very different level with the exact same exp (this never happens for obvious reasons).
You probably just need to make sure both of them are in the same exp level up group.