I have fixes for one and three.
The function error is technically a malformed PDF, the function definition is lacking a bounds attribute which is need to properly execute the function. There isn't anything in the spec to saw what should be done when this error occurs. I've touched up to code so that it will return a valid set of numbers instead of null. The strange part about the problem is that it it doesn't affect the visible appearance of the page. So I'm guessing the PDF encoder has inadvertently left some junk in and my change is more of a work around.
The colour error for 3 is related to the Seperation colour space. This colour space is a bit odd but after reviewing the spec seemed to following the rules but the generated colour was till wrong. I did find a note in the latest PDF specification that that stated regardless of additive or subtractive device, if the named colour could be represented in the colour space it should be used as is and the alternative colour and tint should be avoided. I made a small modification so that if black, red, green or blue was detected for colour name then we would just use it verbatim. I'll have to see if anything strange comes out of QA as a result of the change.
Log feedback during review of the attached PDF in the ICEpdf Viewer:
org.icepdf.core.pobjects.Name convertHexChars
WARNING: Error parsing hexadecimal characters.