I've never seen it do it when you directly drink it from a well (maybe if your hands are bloody it'll do it, but that's understandable). It happens when you fill a water bottle from said well. Its weird, perhaps its a bug.

Yes, that is EXACTLY what I've been experiencing. Really repeating what you said, if you loot a water bottle with water in it or a canteen, if you drink it nothing shows above the germ symbol. However, if you fill it up in a well/drinking fountain (supposedly clean water) even if you use purification tablets the three arrows above the germ symbol will show up once you drink it. I haven'y got sick from it as I try to not use it too much, but it does happen. pilgrim*, it is not the stomach symbol. You're still skeptical, but as Beavis3D as mentioned above, the stomach symbol will show to the LEFT of the health cross symbol once you get close to being full. As seen here:

I used the water purification tabs on the water bottle.

The fourth from the right of this picture: After drinking water, it would have three arrows up like in the picture (an no its not the water one [first from the right]). And no, it was not the stomach sign. PS: This is not a picture of mine, I just picked one online to demonstrate the exact symbol.

Playing on the PC.

Hello, I'm quite new to Dayz, and with the new patch there was the introduction of diseases to the game. I understand that now drinking from ponds without sterilizing the water will lead to cholera, however I'm drinking from a water bottle which i filed from a well and the bacteria symbol has 3 arrows above it when I do so. Even if I sterilize it and take a sip, it still goes up. Can anyone explain what I'm doing wrong here?