I actually used to experience this a lot with many songs that involved a lot of comped jazz-style barre chords, which would result in serious cramping of the muscle between the thumb and first finger. Mr.Dave is very right. Poor form is likely the culprit. It is good to be mindful of your thumb's alignment with the barring fret, as well as how far your thumb extends beyond the neck during normal play, as in when you're not churning out hand mangling barre chords, which, through conditioning, or lack thereof, can have a negative influence on the muscle that is cramping up on you. It's also good to be mindful of whether or not you're exerting more pressure on the barre than what's necessary due to nerves or any other reason.
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