So, we already cleaned everything in rodalon and ethanol, threw everything (media, PBS, cells etc.) away, decontaminated the incubators. Basically decontaminated everything, and started up from scratch. We also did a mycoplasm test twice and they all came back negative.
Together with dapi we also use Acetylated Tubulin antibody and we always see the cells look just fine, so I don't think they are apoptotic vesicles.
We did a new test where we mixed fugene6 and plasmid and dapi stained it. What we saw looked exactly like the dots we see. So probably it is due to bad fugene? The fugene-DNA complexes form, but they don't enter the cells. Wouldn't that make sense?