Here's how it works:
* The prefix is actually "con" which in Latin means "with" or "together".
* The word "ception" comes from the Latin "capere" meaning "to take" or "to seize".
So, "conception" literally means "taking together", which refers to the act of forming an idea or a plan in one's mind.
The "tr" is a silent letter, which developed historically due to changes in pronunciation. It's similar to the silent "e" at the end of words like "have" or "give".
In short, the prefix "contr" in "conception" is misleading, as it's actually "con" which means "with" or "together".