Is col a prefix of collaborate?

No, not at all. The prefix in "collaborate" is "co", and the "ll" is there merely for ease in pronunciatiation.

"col" is never the prefix of anything. It simply does not exist.

You need to watch out for such additional letters, or doubled letters, that are there merely for the sake of pronunciation.

Here are a few more: panicked, trafficked, collapse....
D.A.W.