Lowla, sorry for not seeing your post sooner. I've had a Harbor Freight 10x12 greenhouse for about ten years.

I have a blog about building our HF greenhouse and I try to field questions when I can. I've had folks tell me their GH wasn't fitting together correctly, but so far the problem was always somewhere in the construction process; I've never known anyone who had to drill new holes to make things fit correctly. The HF kits do have their weaknesses (see my blog below) but the parts are, in my experience, drilled correctly for assembly.

My advice (and sorry it's so late) would be to take some of the frame apart again and get it to the point where you can move the pieces around to make sure they are square and plumb as you go. (You might have to take the roof off, I'm not sure.) The aluminum frame is quite soft, and it's quite possible to put it together with the pieces "a little bit off" from square. Unfortunately If you start out with the parts a bit out of square, as you go further, each new layer of parts can compound the problem.

You may have to disassemble some of the frame to start correcting, but you won't have to start all over. You can remove some pieces and get to a point that will allow you to merely loosen the nuts...not remove them...and ease the pieces back into square. At the early stages of assembly, there is flex and "wiggle room" in the frame as you're starting. Use a level as you go. Make sure each vertical post is truly plumb and square before you tighten down any braces.

Then your panels will fit into the openings as intended. I hope you can fix the problem!

My blog for my own 10x12, if it helps: Building our Harbor Freight Greenhouse

Adding just one more post...even if you found a way to make your frame work as is, please do take the time to skim my blog, especially the parts about Adding the Panels, and fastening the panels in with screws. (If you scroll all the way to the bottom of any page of my blog, you'll find a list of links to each section.)

The biggest problem with the Harbor Freight greenhouse is that the panels can easily blow out in a strong wind. If you only use the clips provided in the kit, and don't add a screw or two into the frame for the panels, chances are pretty good you'll have problems keeping your panels attached. That can either result in the annoyance of looking for your lost panel...or, sometimes, the loss of the entire structure, if the wind is bad enough, and the soft frame becomes damaged.

Sorry to sound negative, but a little care up front can make the difference between having a greenhouse you enjoy for years, or having a very unhappy adventure. (I want you to have the former experience, not the latter!) Best wishes to you.