Take this simple flow:
label scene1:
# menu is just to give a concrete example
# but even without it, you can reproduce the bug
menu:
"A":
jump .a
"B":
jump .b
return
label .a:
return
label .b:
return
It generates the following graph (passing -hide-screens to simplify):

Now replace the second jump with a call:
menu:
"A":
jump .a
"B":
call .b
return

The path to .b is now missing.
Now use call on first statement only:
menu:
"A":
call .a
"B":
jump .b
return

This time, the path to .a is missing.
Finally, use call everywhere:
menu:
"A":
call .a
"B":
call .b
return

and nothing appears.