When you disenchant a crossbow with Multishot, and it has an arrow inside it during disenchanting, the game still sees the arrow as a Multishot arrow, and as such shoots 3 arrows from the disenchanted crossbow.

This is displayed in the video attached to this report (sped up due to file size limits)

The game is only modded with Optifine, which only has some lighting editions and should not effect the game server itself