Seems to me that some scientists today take the "observation and articulation of what has been observed" (to quote Bohr) under methodological naturalism - and then promptly turn around and present it as "explanation".
That would be like removing the leg of man, subjecting it to rigorous research and then turning around and declaring that the observations made on the leg explain the whole man.
Nature is but a part of "all that there is."
This is an observer problem in an epistemological sense, which is other than the observer problem as described earlier where the behavior of phenomena is passive to the act of observation itself. I see two unique issues--or do I have that wrong?