One thing I do when writing a program and emulating or commissioning it is create a DINT tag for Ladder_Is_Running and in the beginning of the main routine MOV 0 to it.
Then in each subroutine OTE Ladder_Is_Running.1 for the first, .2 second and so on.
Then in rung before the above MOV 0 I put a line of XIC L_I_R.1, XIC L_I_R.2, and on until the last used bit ending with a NOP.
When online if a rung is being scanned and turns on its bit then that XIC will show true. If one never shows true then the call is not there or if conditional not being called.
When troubleshooting an existing program to see if a subroutine is being scanned I do the same with only a single bit.