Thanks for providing your files. I am happy to report that there's a simple solution to your problem.
The Skyline Targets tree has a hierarchy Molecule List > Molecule > Precursor. The way you have imported your transition list, the column of molecule names is being interpreted as a column of Molecule List names, so you have many molecule lists, each with a single molecule, whose names are created by Skyline based on the Q1/Q3 values. But these Q1/Q3 pairs are not unique across your transition list, and the result is that some molecules appear in more than one molecule list, which Skyline wasn't expecting.
If you simply declare that column of names to be the "Precursor Name" column at import time, you will have a single (automatically named) Molecule List, and a few hundred distinctly named molecules below that, each with appropriate transitions below that, and everything will work smoothly from there.
We will work on improving this error message, thanks for helping us improve Skyline!