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Tuning issue

I was playing my bass last night using a headstock clip on tuner. I made sure I was in tune and started playing. I noticed when playing a C at the thris fret of the A string it didn't sound right in tune. In between songs I checked the open tuning and they were still on. The notes at the 5th fret were also in tune. However notes played on the 3rd and 4th frets were a bit sharp. Has anyone ever noticed something like this before? Could it be a neck issue? Being out of tune is one of my pet peeves.
 
A lot of clip on tuners have modes, like chromatic, bass, guitar, ukulele, violin.....

It'll work on chromatic for every note or bass for open strings only. See what mode it's in.

Clipon tuners don't read fretted notes very accurately in my experience. Handy for checking open strings' tuning on the run, but use a better one for intonation setups,a strobe preferrably.
 
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All of the above mentioned points could be a problem. As I first read your post, my mind jumped to the possibility that your nut slots may be too high, as that is a problem with one of my Squiers.

But then I remembered the problem with using any tuner to check fretted notes (even really accurate ones)... And that is the fact that bass guitars use equal temperament for fret spacing. Even with the most perfect, accurate fretwork, various frets will still be ,technically, slightly out of tune.

http://www.guyguitars.com/eng/handbook/Tuning/tuning.html (some good info on equal tempered tuning)

So as long as you're not squeezing too hard, your nut slots aren't cut too high, and your open string intonation is set, then it's just a case of "Situation Normal".
 
It takes a lot of pressure to do this on a bass. I think it's more likely that he would be unintentionally bending the string to the side.

yep you're right, sorry about that and my previous quoting of your post, i don't know why i remember having this issue, i just tried it and with i clip on i can barely get the "needle" to move by fretting harder. must be a hold-over from my skinny-string days, haha.