This happens when splitting a proposition that has a "part after arrow" (i.e. one with at least one enclosed child/indented proposition), after a clause item that is not the last.
E.g. situation:

• Proposition "1" "2" (two clause items) – one downward pointing arrow
• Proposition "3" – enclosed by "1 2 4"
• Proposition "4" – one upward pointing arrow

If you now select "Split Proposition after this Clause Item" in the first ("1") clause item's context menu, the propositions "3" and "4" are gone. Instead, the following result is expected: