The incorrect part is that you are getting all your files into a list without any filters, apart from the fact you only get .pdf files. And then you're using that list to merge the files without any pre-processing. So, clearly, it will merge all of the files you get in Get files in folder.
You either need to apply some file filters there (you can include several file names, separated by a comma), or you need to Create a new list and then use a For each loop on %Files% and only add the relevant files to this new list. And then use the new list in Merge PDF files.
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