This is an old and strange bug, which is not that harmful, but rather annoying.

One can use the following python code to illustrate it:

from os import system
system('fish')

In fish type exit and see the message:
Job 1, “ipython” has stopped
Then you need to call 'fg' to put the program back to foreground.

The same happens if I use subprocess module of if I use another languages (lua: 'os.execute "fish"').