It would be alarming if it wasn’t 
But setting the intonation is adjusting the fine difference between the fretted 12th fret and the harmonic (or open string).
Properly intonated they should all be in tune at the same time.
But most likely the fretted note is a few cents off.
The harmonic is irrelevant unless maybe you play a lot of harmonics… but what most of us care about is the open string and the fretted notes. Depending on the height of your action, the size of your frets and how hard you press on strings, the fretted note will generally be slightly sharp vs the harmonic because you are stretching the string by pressing on it. I have a Yamaha guitar that for whatever reason, takes an extremely light touch to not bend notes noticeably sharp! Obviously it’s not as much of an issue with heavier strings on a bass unless you have a death grip on the neck 
So, I did the intonation on my P-clone a few weeks ago (call it 6-7 weeks). It was set up perfectly.
Yesterday, on a whim I checked it and it was flat on the E, sharp-ish on the A, sharp on the D and fine on the G.
I have GHS Precision flats on it that are just over 2 months old. I use the plug-in tuner on my Zoom B1four
Any ideas? Are the strings that susceptible to stretch? Could the tuning machines be giving me gyp?
How is the truss rod?
Humidity and temp changes so much with the seasons that I need to tweak mine every 6-8 weeks, and that of course will likely cause intonation changes.
I live in the Barrie area and with the seasonal weather changes recently have had to tweak the intonation on my Yamaha TRBX 504 about once a month.
Layering helps… LOL
What is layering?
Man I tell you, my necks are moving daily here in NY. My room is dehumidifier controlled (as best it can be, still cycles of course) and I am tweaking a LOT across a few of my newer basses.
Sorry, I was just being a smart-aleck with the reference to layering - putting on my clothes (or bundling your bass) - in response to a shift in the weather. My failed attempt at humour…
Nothing to see here. Move along, please! 
i actually have 2 basses lying on my couch separated by pillows so i guess that’s layering 