Just one from my personal experience: Conda installed Python having different compilation flags than official and distro Python builds, breaking ABI and causing native extensions built against official Python to crash when loaded in Conda Python.
A few times a year our office loses power, which causes the machine we have running for data evaluation to crash. There seems to be about a third chance for that to damage my Anaconda installation.
Last time I could only solve it by deinstalling everything and reinstalling an updated version. Took ages to get all packages running again. Luckily my code still works but now I get depreciation warnings (and not in my code). Who knows what will happen next time. It only took like a day I needed for actually working with the data as well... urgh.