CC's
If I understand your questions....
I believe the .15x has a pressfit wrist pin. You did not see any retainers or brass or plastic caps, right? The comments below are based on this assumption.
The pin could not slide out into the liner unless the liner was mislocated, as you discovered. However, even with the liner properly indexed, if the pin is loose, it may "slide forward" and score the liner.
Clearly, this engine was taken apart and not put back together correctly, based on your observations.
At this point, I would suggest--if you have not done so already--having it taken completely apart. Then cleaned to remove all of the castor baked onto it. Use a process that does not abrade any metal from the parts. Then inspect the liner for damage, especially at the ports where the pin may have hooked it. Check the piston for damage. Either fix the damage or replace the parts (or engine). Next, you have to find out why the pin is floating around. If the pin will not seize in the piston without protruding, then the parts are not going to work. I can't recall taking this particular engine apart, but I think what is needed is to install the rod into the piston with the proper face oriented to the piston baffle, and insert the pin in the correct direction. (The press fit side should be forward.) Then lay the assembly on a shaped softwood buck (2x4 would be good) and using a drift punch, tap the wrist pin into the piston firmly. You need it tight, but without distorting the piston. Then reassemble, ensuring that the baffle is on the bypass side. Finally, the liner orientation must be correct. The exhaust port is the one closest to the top of the cylinder. And the head goes on with the baffle relief closest to the bypass side.
Once together, and with the plug out, check for excess friction. If all is free, try running it.
Good luck. I hope it is not damaged, and you can find a useful home for it.
Divot McSlow