Overwintering is tye main cause usually, I had the same problem with citrus in pots then when I examined the pots the roots were dead. Not all of them though.
The root rot is not from water stagnating, but by a fungi called Phytophora. Even if you have sterile mix in pots, rain splashes from ground soil can reach the pot soil.
Or īn my case I used store bought composed which I didn't sterilised.
To kill it you need to drench the soil with a fungicide or take the tree out wash the roots and change soil. Once the fungi in in the soil it will attack when wet and cold conditions occur.