Editing issues

Take care that the first track in the selection is the focused track (track name highlighted). Depending on how you make a multi-track selection, that may not automatically be the case, and SONAR will always start the paste at the focused track by default.
 
Also be aware that there's currently an issue that if the selection has empty space before the start of any clip content, that space/offset won't be included in the Cut operation. Workarounds in that case are to Drag or Process > Slide the selection instead of Cut-Paste, or use Copy-Paste, and then re-select and Delete the original selection.

Can you give a specific example? It's not really clear what 'scrambled' or 'all over the place' means.

I mentioned this in another thread, This has happened to me over and over with cut and paste of very basic midi songs.  And one would think that after 12 years I sort of know what I'm doing,,, but things changed in the X series for the worst I think. Possible the Take lanes stupidity.  
I find a good song to work on and the first thing I do is re arrange it to my liking.
 
Say we wish to copy 4 measures to repeat the intro  and paste it after the original. 
no problem, Just copy 4 measures. make a 4 measure hole and paste. ( or use Slide over option)   Bingo..
If your lucky this will work just like a logical person would imagine it should.
Other times this makes the big mess just like the OP is experiencing.
I'll add here that I will at this point try all 3 paste options with the same results. 
It might be that unless all the notes are just so in the measures that it scrambles everything into a big mess,, often with a track overlaying it self and playing double the notes..like the verse and chorus at same time. 
And sometimes the mess isn't even in the measure you just pasted too,,,, it shows up way down the time line??? that's real weird.
It certainly never happened in 8.5 and back as I did a lot of this work in that version.

agggg....  Thank you!!