Double counting an axle is a critical failure for an axle counter. It could keep a track section blocked until someone comes to fix the axle counter. Even worse

Double counting an axle is a critical failure for an axle counter. It could keep a track section blocked until someone comes to fix the axle counter. Even worse it could unblock a track section while there's still (part of) a train on it. If you're worried about double-counting an axle you probably need to design your axle counters better.