Multiple Counter glitches occur in Pokémon Red, Blue, Yellow, often in which the move Counter hits when it is not supposed to.
Counter after using an item
Counter hitting after Lorelei healed her Cloyster with a Super Potion.
If the last attack used in memory was a Normal or Fighting type move, was not Counter and dealt damage (even if it was from another battle) and the opponent uses a healing item, Counter will deal twice as much damage as the last attack and it looks like the user is countering a healing item. This does not work with Bruno's X Defenses (and probably other X items) as it is lower in priority than Counter.
This glitch may also occur the other way around (the enemy countering the user's items). The player doesn't have to use a healing item, as it works with X items. If Counter is used in succession, then its damage will 'double' every turn.
Counter after a switch
Counter hitting a Pokémon that switched out.
If you meet the last attack conditions in counter after using a healing item section (or simply select the move and not necessarily use it) and switch Pokémon, the opponent's Counter will 'Counter your switch' and this can be repeated for more than one switch if the opponent keeps using Counter. Likewise, if the cursor is last moved over to a move which cannot be countered (e.g. Ice Punch) Counter will fail after the switch.
Counter after a turn where the Pokémon does not move
Counter hitting after Cloyster cannot move due to paralysis.
If you meet the last attack conditions in counter after using a healing item section and the foe cannot move due to paralysis (or possibly a freeze) then Counter will still be able to hit.
Link battle desynchronization
On the user's side, the opponent's Counter will hit the user provided that the last move selected (and not necessarily used) from the Fight menu is a move that is possible to be countered (e.g. Body Slam). However, for the other player's game Counter will only work based on the last move that was actually used. This way, it is possible to cause link battle desynchronization by selecting a different move (one that can be countered if the last move could not be countered, or one that can't be countered if the last move could be countered), not using it, and switching.
For example, the player may use Body Slam and the foe may Counter it. If the player then opens the Fight menu to select Ice Punch, closes the Fight menu and switches then the foe's Counter may fail according to one player (the player that put the cursor over Ice Punch) but work according to the other player.