You probably got used to hearing a sharper E and A, or your tuner is busted.
Next time, tune your D and G strings, and play the octave E on the E string with the E on the D string (should be the same note) and compare which one is off.
Same with the octave A and the A on the G string.
Next, do the same thing but having tuned with the tuner before hand. See what's going on that way. If the notes play in unison, then your ears are messed up and the tuner is correct.
