You have two points that I think are reasonable to raise: (1) is there a mistake (intentional or not) in the assumed margin of error in the measuring equipment? (2) is the DRAM caching behavior taken into consideration? Neither of these two points have anything to do with FPGA per se. Now by including the enchilada word "FPGA platform" into the fray (whereas it was clearly not the intention at the beginning), I feel like you are making things up as you go, which is unfortunate since part of your argument is valid.
I chose the word "FPGA" to match the terminology of the paper which uses the word as a synonym for the Data Acquisition System.
If so, that's a problem with the paper in itself. (I haven't read it.)
True, but your essay confuses acquisition with storage. As a rule, by the time the data is stuffed into a DRAM somewhere, it's already been timestamped. If you're right, and it hasn't been, then, yep, that's (a) problem.