Does some of the sprites in png format are 2x scaled?
Libresprite doesn't support some chunks of Aseprite so can't be absolutely sure but you don't use indexed color mode? https://www.aseprite.org/docs/color-mode/
If you use predefined pallet it will prevent you from accidentally creating new duplicate colors and etc. and will decrease the size of art. Png also supports indexed mode but only up to 256 colors pixelart usually doesn't use more than 32 ;)
In Libresprite it can be changed through "Sprite > Color Mode > Indexed" what is about Aseprite? Don't know but almost sure it will be in the same place