Hmmmm, well I wasn't actually trained as an oceanographer so I was mainly there to run the gas chromatograph. But the topics I think I found most confusing were things like the Revelle Factor. I mean, I can sort of understand its application, but its derivation and what it actually is doing is still a bit of a struggle for me. I also found that the complexity of various relationships between density, temperature, salinity to kind of be overwhelming since they are quite complex and ultimately drive a lot of the currents in the ocean.
I never fully understood what the guy doing the 4He stuff was doing.
One project I was on was using a tracer to assess gas exchange in an estuary. I was responsible for collecting the samples and running the GC again to test for the tracers we were looking at which was pretty straightforward....but the modeling the grad student who was running the project did was waaay out of my comfort zone.
Don't get me wrong: I learned a LOT during that year but really oceanography is NOT simple. Especially for people like you and I who are not oceanographers.