Sounds like your intonation is out. Intonation is your guitar being in tune with itself. So when you play an E, be it the low E string, the high E string, or an E anywhere on the fretboard, in theory, they should all be perfectly tuned to E, just higher or lower in pitch.

When your intonation is out on an electric, there are usually adjusters in the bridge or saddle that allow you to adjust your intonation back in tune.

Unfortunately, acoustic guitars have a fixed saddle/bridge, so adjusting the intonation is not so easy. If the guitar is worth more than $300, you'll want to take it to a luthier/repair shop and get an estimate on getting it fixed. You can try yourself.. watch some YouTube videos, but i wouldn't bother if it were me... just let a pro do it.

If the guitar is a cheapy, worth less than $200 with no sentimental value, then put in behind your car in the driveway, back over it, then pick it up, take it to your spouse and show them the guitar with tears in your eyes... I guarantee you will have a brand new replacement in 8 days! ;)