If the guitar doesn’t normally have tuning problems then it could be old strings. When they get old they can sometimes seem almost impossible to tune properly.
If you are going only by what the tuner is telling you but it still sounds out of tune – to some extent this can be normal. The guitar cannot be tuned perfectly along the whole neck, it’s not possible. Guitar tuning is a bit of a compromise and small imperfections are to be expected. If it sounds really bad then something is wrong, possibly the intonation or a warped neck perhaps.
If you find a string is getting muted when it’s in tune then this could be the bridge or nut needs adjusting / fixing, or a neck or fret problem. You can also get this problem if you change string gauge, the guitar might need some adjustment. This happens because different string tension will slightly bend the neck and can force a fret to touch a string.
If it’s nothing obvious that you can see causing it then it might be best left to a guitar tech.
Thank you for the reply.
This is really weird, because I bought a Taylor GS mini. I had the Tech. put warm strings on the $800 guitar and to check the action and the truss rod. Overall check to have the guitar to be the best it could be. The Low E string-Shows to be tuned but it sounds flat or muted and all the other strings sound ok. I am not sure about keeping the guitar, with a bad sounding string. I just don’t understand how this can happen. Do you have any other thoughts about this?