The tool used to calculate Alomar's defense is Total Zone, and it is garbage but the only thing available during his time and prior. Any defensive measurements from that time period have to be taken with a grain of salt and players today are evaluated much more accurately. I feel like you've been told all this already.
There's also the possibility that Alomar suffers from Jeter syndrome and just isn't quite as good as we thought, because of some flashy plays he made in the field.