When building a new tunnel, the track most recently selected will be put inside of that tunnel. Technically, there is not much difference in between "normal" ways and elevated ways and there doesn't seem to be an explicit check for the elevated system type, so when the last selected way was an elevated way, it will be built inside the tunnel.
How to reproduce:
1. build a tunnel
2. select an elevated way
3. enter underground or sliced view mode
4. attach to that tunnel
5. The new tracks will use the elevated way inside of the tunnel