What can i do to prevent this (cause i want to be able to manage the clients ip traffic).
You could put a 3rd ethernet card in your Mikrotik gateway box, connect the Squid box to that and add rules there
replace the LAN switch with a managed switch or put another mikrotik device in front of it
Use DELAY-POOLS in squid
Put a second ethernet card in the Squid box and put it between the Mikrotik and the ISP ( you need to set it up properly for security,reliability)
Problem with putting the Squid box in front of the Mikrotik is if it dies it will stop the traffic flow ( consider ethernet card with "bypass" ).