Here’s some stuff on polyurethane finishes that I have found out today. Some of it obvious some not. Although it might not solve your problem outright it may arm you with some basic info if you need to speak to Fender or one of their outlets at sometime down the road if the problem persists and you need to get it looked at.
First, there are several types of polyurethane finish. Oil modified which is solvent based and the most common it does yellow with age. Moisture cure, the most resistant and hard wearing, aging and non aging are available, mostly used in specialised pro situations, not common. Acid cure, very specialised and not common. Water based, most common non yellowing and expensive by comparison. There is no easy way to tell which you might have easily. Only Fender can advise you on that.
Polyurethane is a polish as opposed to a lacquer the main difference in this situation being that successive coats lie on top of each other and don’t react with previous coats to form one layer as lacquers do. This fact could be a lot to do with your problem.
Any contamination between coats can cause bad adhesion either on the sealer or between coats. Normally this would manifest while the finish was being applied, but can if the problem is slight not be detected. If a coat of polyurethane is layed up on top of any contamination it will not adhere correctly. Grease, oil, water can all cause an issue here and is not uncommon. In severe cases crazing, checking or dragging are evident. If one of these problems doesn’t show it self during application it can later on down the road. Similar problems can be caused by shooting a topcoat over a previous coat that has not fully cured. As polyurethane is an impervious finish it will trap solvent in the previous coat and not allow it to fully cure and it will be unable to gas off. This can lead to printing in the build up coats as although they may be fairly hard they will never fully harden!!! In normal cases this would be detected during application but if the problem is slight it can go undetected and can also happen selectively on the finish or in patches.
This info has been supplied by a guy who knows his finishing and who I trust so although I have little experience with polyurethane I would trust it. If anyone else has further info please chip in or correct any inaccuracies. He did say that such a problem would be rare but not impossible and suggested reasons are his best guess only.
Now the bad news, the only solution strip and refinish. The only people who can confirm any of this would be Fender as they know what they used and how it was applied.
I should keep a close eye on how finish as a whole holds up and hopefully if you need to speak to anyone about it in the future they will have to work harder to convince you its your fault not theirs!!!. Sorry I can’t supply a more positive solution.