Hitmontop is coded to use sucker punch vs haunter as it's super effective (Npc pokes will always use super effective moves if possible). Since it's not super effective Vs typlosion then it will choose to use either a different move that's super effective or if no such move exsists then presumably it's picks the strongest neutral dmge move(usually stab). In this case the alternative move hitmontop is using Vs typlosion isn't a priority move.a

 

Here is a full list of moves that have a priority change. +X moves happen 1st -x moves happen last

 

Should 2 Pokémon use moves of the same priority tier then the fastest will go first (usually both moves are priority tier 0)

What move did the opponent use while you used flamethrower?

It was a Gradevoir using Psychic one of the times. But my Haunter got evolved to Gengar, and I have not encountered anything weird since :/ Thanks for all the support and answers though :)

Gardevoir can reasonably outspeed haunter