So I'm trying to do custom scenario with free rides and the entrance fee is not being collected, is this a glitch or is there a way to solve this?

You mean the entrance fee to the park? That shouldn't be a problem. Of course, you may not create your scenario so that zero dollars is a "fixed entrance fee".

Are your guests coming through an entrance or being generated in the park? If you have no entrance there is nowhere for them to pay.