I am configuring a CISCO's 4331 router password, in Packet Tracer. More specifically I use the command enable secret weakpassword. This command uses by default MD5 to hash the last string (i.e weakpassword) .

The thing is that when I use an online MD5 Hash Generator for 'weakpassword' I get the hash e04efcfda166ec49ba7af5092877030e and when I use the pre-mentioned command I get the hash $1$mERr$A4DAiA6cbNxoV7Y2eEVOA0 which apparently is not the same.

Why are the hashes different?

CISCO explicitly mentions that:

Enable secrets are hashed using the MD5 algorithm. As far as anyone at Cisco knows, it is impossible to recover an enable secret based on the contents of a configuration file (other than by obvious dictionary attacks).