what you have here is a start of a common illness among guitarists (and tennis players alike), tendinitis (or tennis elbow), if you feel uncomfortable, stop immediately, because if you hurt yourself, there's no turning back...
What you need to do is use another way of warming up (no scales, no legato, play chords, without stretches...) stop playing if it hurts... If you are patient, everything will come back to normal... You should see a sports doctor though, so you might hear some advices.