I assume you used traditional-digestion cloning method. Was the vector single or double digested?if it was single digestion, it highly recommended to switch to double digestion, if it possible, to avoid vector self-ligation. Have you checked if your vector was linearized after digestion? Make sure your restriction enzyme(s) works properly and the insert was digested by the RE.

On the other hand, you can try Gibson to construct your vector. Check this kit. It works very well with me.

Good luck

https://www.bioscience.co.uk/userfiles/pdf/Gibson%20Assembly%C2%AEUltra%20Kit%20Quick%20Reference%20Manual.pdf

@ahmed it's single digestion that I'm doing. I ethanol precipitate after digesting with a single enzyme and then add the next. Yet in gel I'm getting a smear. I'll try looking for appropriate double digestion protocol with the thermo enzymes that I'm working with. Thank you!

If PCR is showing the presence of your gene of interest (and assuming you have the right primers and controls so this is a real result) then it seems that perhaps you are having a problem with your restriction digestion analysis. You might take a few putative clones that are positive by PCR and do a good DNA preparation and then a careful analysis perhaps with other enzymes.