"Clashing" is where one COB or agent has the same class number as a different COB or agent, and they are injected into the same world. The scripts mingle and cause the COBs to do crazy things, and then the game crashes. To avoid a clash, you should check what class numbers all of your downloaded COBs or agents have before you inject them.
To check the class numbers, you can go to this wiki's own list of known C1 class numbers, or go to Bibbleworld and check the Creatures 2 and Creatures 3/Docking Station lists there, or go to the current CDN.
Also, it is where one breed uses the same breed slot as another breed. If you try and install both without changing the breed slot (a tutorial on this is available at Creature City - archive), it will overwrite one.