Hey thanks for the explanations, I gave it another shot and did manage collect some samples!
I think part of what confused me is that if you are targeting a sample, but not zoomed in enough (fully?), pressing E again will zoom rather than collect even if there is the targeting reticle around the sample. Some shapes are also more distinct than others (the letter lookings one are way easier than the polygons). Whatever it was, once you get a grip on it then it becomes way more doable and pretty fun!