Tie on same side of staff/ledger line as augmentation dot = collision
When a tie appears on the same side of a staff/ledger line as an augmentation dot, the tie goes right through the dot. In looking at professional engravings, the start point of the ties in this case are usually placed just above the dot if it is above the line, or just below the dot if it is below the line.
Here is a graphic comparing MuseScore's current behavior with ties adjusted similar to the engravings at my disposal:
The ties in question appear in measures 3, 7 and 11. For the ties in measures 3 and 7, I made the adjustment by moving the tie's start point up using 4 presses of the up arrow key. In measure 11, I moved it down 4 presses instead.
I have included the MuseScore file as well for your reference. I am using MuseScore nightly ff2b92c on Kubuntu 14.04 64-bit.