Using the current Paperpile Annotations Viewer and using a PDF with annotations generated by another PDF Reader (in this case PDF Expert 6 by Readdle on an iPad), the MarkupText is often missing words or parts of sentences at the beginning or end.
The PDF’s contain proper annotations (subtype: Highlight) and using Adobe Acrobat DC, selecting the highlight and doing rightclick->copy text grabs the entire text. It seems like Paperpile/MetaPDF is mis-interpreting the boundaries of the annotation somehow?