Can you send us your Skyline document?

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including extracted chromatograms.

If that .zip file is less than 50MB then you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick

uploaded. please let me know if you have any more questions

It looks like you only uploaded the .sky file.
Can you upload the .sky.zip file that you get when you do "File > Share"? The .zip file contains the extracted chromatograms, which are necessary in order to reproduce this problem.

Uploaded.

Sorry about the slow response.

This error is happening because some of your replicates (e.g. "Pool01") have chromatograms for both your positive and negative Asparagine precursor (131.0462[M-H] and 133.0608[M+H]), and other replicates (e.g. "pool_group_1_NEG") have only one or the other precursor in them.

The "Apply Peak To All" menu item works by trying to find peaks in the other replicates that share characteristics (retention time, transition peak area ratios, etc) with the chosen peak in the current replicate. It looks like we could be doing a better job of handling the case where some replicate are missing some chromatograms, but the fix would probably be that Skyline would skip over these replicates.
I am not sure whether we will be able to improve this behavior. For now, I would recommend that you create separate Skyline documents for your single and multi-injection replicates.

I hope this helps, and let us know if anything else in Skyline seems to be behaving weird.
-- Nick