City of Houston / Occupancy question

Hoping for some clarity here as I am totally lost.

We leased a new warehouse in Houston and applied for our CO. We were initially only using the space for overflow storage so we had nothing in the space and applied for our CO. When inspectors arrived they said we had to be setup like we were going to be operational, everything down to the desks. They would not accept it was just for storage. So we rescheduled and sped up our time frame and started bringing in product, shelving etc. We had some minor electrical ( added a few outlets ) and a sink so some plumbing too. When my electricians/plumber went to apply for permits they said we didnt have a CO so we could not get permitted for that work. Called the city back and they said you need to be setup fully to get a CO . So can someone help me out here……I cant get a CO bc I am not setup for business but in order to be setup for business I need to do a some electrical and plumbing but I cant get permitted for that bc I dont have a CO??/ WTF???

Help please….

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Also, am I in any trouble since my plumber and electrician did the work ?