It took me some time to find the best cleaning solution for LCD's, like fingerprints. Never use cotton swabs, or 100% isopropyl alcohol (IPA). 100% IPA evaporates too fast and you can make the little spot like a fingerprint, larger. What I do is the following: Mix 50% IPA with 50% demineralised and distilled water. That solution is strong enough to clean the spot, and will not evaporate too fast. Then use Anti-Static Foam Swabs for cleaning BGA/PCB (Cleaning Swabs CM-FS712 CleanTip) and take 2 pieces. Put less then a drop (as little as possible) on 1 foam swab, and remove the spot. Particles of the IPA mixture will stay on the LCD. With the other dry foam swab, remove the rest of IPA mixture from the LCD. In that way, you can perfectly remove the spot.
I had the same problem when installing a new digitizer (black) with home button preinstalled. The home button was working outside the ipad, but not working when fully installed. Deinstalled the digitizer and put kapton tape on the home button flex cable. After that everything was working fine. See picture below where I put the kapton tape.