When Using (File - Place) illustrator applies an unwanted clipping mask which is not present if opened normally.
I import lots of vectors and other files from various places on my computer and everytime I use the (File - Place) feature the vector I import has this unwanted clipping mask.
I find myself clicking ungroup - release clipping mask - ungroup - release clipping mask until the image is completely destroyed and I'm left with a bundle of gradient boxes and an outline of the original shape.
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Robert, what format do your placed files have?
If the are in PDF — then it's OK.
Illustrator can only OPEN files in .pdf if they were created in Illustrator itself and have proper settings. If you try to open PDFs from other apps — AI will have to IMPORT them, with the consequences you probably are seeing: clipping masks.
I can advise AstuteGraphics VectorFirstAid plugin to clean such files.