Probably like Roxy said its your plastic output not being correct,

Probably your Z is to low wich makes your first layers correct, But once its at a higher height it still shows the error,
Or you didnt measure your Plastic diameter, Wich you could simple increase instead of doing your E axis calibiration,
or if you do have a precise measuring tool (Atleast a caliper of 0.1-0.05mm tolerance) you would be better of calibirating your E axis again.

When your pushing out more plastic you will probably see that your first layer doesnt look that nice anymore, so you will also have to get your Z endstop hit higher, But you adjust that when your printing and modify it then.