How big of a problem is this?

When i germinated my seeds i chucked my autoflowering and photoperiod in together, during sprouting i repotted the plant i thought was auto into a 3gal. Unfortunately, i repotted the wrong plant, leaving my auto in a 6inch pot.

What kind of problems is this causing? Is it going to have a big impact?

I can't really repot now, on day 26 of flowering, stress, stunted growth both issues.

you should be fine, might effect total yield a little, but no issues should arise. Enjoy your grow!