This mainly occurs when loading mp3s, which are currently not supported by libsndfile. This is due to change in the near future, but in the meantime, we revert to audioread to decode mp3s and other unsupported formats if possible.
I wouldn't say there are side effects to using audioread instead, but there are features that it does not provide, notably working with stream data (instead of files on disk) and block-wise decoding. Audioread can also be much slower than libsndfile, but that will depend on the specifics of the data being decoded. There may also be differences in supported bit depth, but that is also codec-dependent.