Seemed odd when looking at the picture. Though either way it probably isn’t a big deal, I agree with Sara the bees will fill in and the wax covering is probably strong enough to hold.
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Sorry your Flow Frames arrived like that. I’m glad you were able to figure it out at re-assemble it without any problems. I like your church pew description 
For anyone else with this unfortunate issue, the video’s to fix any mis-aligned, loose Flow Frames are here -
http://www.honeyflow.com/faqs/fixing-bent-misaligned-complete-flow-frame-re-assembly/p/180
From your picture I’m unable to see what you mean. I think you maybe referring to the top of the cells and the fact that they aren’t all horizontally aligned (if you were to lay the Flow Frame on it’s side on a table for example).
This is from Stu -
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The cells in Flow frames and in natural honeycomb slope upward. You can see this at the end-on view you get on the clear ends of the Flow frames. Therefore when you are looking at the face of the Flow comb to see if the cells are aligned, you have to tilt the top of the frame toward you (or the base away from you). If you don’t slope it like this it does look like the cell walls are out of line.
We purposely made sure the walls of the cells do not actually meet. There is a gap between the walls to ensure no bee’s legs are caught if a bee is down a cell when the mechanism is operated. The gap is filled with a beeswax wall which can be chewed away if a bee is caught. This gap also makes it look like the cell walls are not lined up properly.
I would encourage Flow owners to insert the key in the top slot and turn it then put it in the bottom slot and turn it again, repeat the process until you feel familiar with the change in the cell arrangement. When the key is in the top slot and turned, have a good look at the comb - from a tilted angle view the cells should look aligned.
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