The name of the publication might help here as would the version of PDF the publication uses. If you are attempting to read the magazine using calibre's viewer, that involves a conversion from PDF to ePub which is, in most cases, not a good idea. Trying opening the PDF with a PDF utility and see how it looks.
If you are able to read any of the magazine, DeDRM has done it's job so I would agree that it is not a problem with that tool.
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