Well, I'm pretty new at this program, so maybe there's a simple explanation ... BUT ... I'm getting a bizarre printing error I haven't seen in my 30 years of using Macs: I'm working on an electronic (video) signal-flow diagram in Pixelmator 3.4.2, OS X 10.11.3, composed of rectangular shapes, simple text, and lines (arrows, really). When I did a test print, a lot of content was missing. I got most of the text, some of the lines, and only one of the dozen or so rectangles, and only three of its four sides at that. The items that are missing seem to be mainly the most recent additions. I tried increasing the width of the lines, up to 5 pixels, thinking maybe they were too thin, but that didn't help. The print preview image looks the same, or nearly the same, as the printed output.
I experimented with selecting some items and choosing "Bring to front" before using print preview; this affected which items were visible, but I couldn't find a setting that made everything in the diagram visible. Large parts were still missing, no matter how I set it.