Most likely the tube at the stem area wasn't fully seated into the tyre. This causes some of the tube to be lifted off the rim and it has to squeeze round the bead of the tyre to expand. This ends up stretching the material thin enough that it separates from the stem or opens up a hole.

To prevent this, don't start & stop mounting the tyre at the stem. And when you're done, push the stem as far into the rim/tyre as possible. You should be able to see a bump from the inner-end of the stem pushing outwards on the tyre-tread. This makes sure that the tube isn't caught between the tyre and rim.