I was looking to rent an apartment and I had the move in date set for May 30th. Now one of my roommates bailed on me. I was trying to talk to the new apartment about going to a smaller unit but with the price now it would be cheaper for me to stay at my current unit. My question is since my move in date is more the 60 days out and the unit I wanted to rent at the new place is still occupied can they really still keep my deposit. When I signed the papers they said they can only hold the unit on a deposit for 45 days.

Hmmm. I really don't know about that.

I see several issues here.
First, you havn't moved in yet.
Second your expected move in date is end of May.
Third, the people in there havn't moved out yet.

Well, your projected move in date is two months away. So you really cannot complain about the people not moving out yet. So I think the rest of this relies on the current lease.

You say the agreement, which since you signed it I presume is really a lease (more info helps), says 45 days. That may be as the Colorado Landlord-Tenant laws have 30 days as the default period if no time frame is specified, but a maximum of 60 days. BUT, you havn't moved in yet. So there is no cause nor reason for them to hold it.

I have a sticky note in this section of the forum, I suggest you read it and then go to the county courthouse and get the contact information for the community legal aid. They can certainly help you figure this out. Also, you can always verify the statutes quoted in the sticky. In fact I strongly suggest you do that.