I once owned a one off G&L artist guitar. That thing would not tune. That guitar got passed around to a few players I knew well. Everyone came to the same conclusion. Something just wasn’t straight with that guitar.100% Only on rare occasions is the guitar the problem. Physically tuning your guitar to a reference is just like learning chords, intervals, rhythm, etc. on your instrument. Stretch new strings until they essentially don't go flat, tune up to pitch and adjust the saddles to get the best intonation possible. *ALSO* don't press so hard you push notes sharp.
I haven't had a single guitar with "tuning problems" once I knew a bit about tuning.