Grinding/vibration under load

I am getting a strange grinding/vibration through the pedals on certain gears. I notice it when in the 2nd and 3rd largest cogs in the back and the big ring up front. Originally I thought it was cross-chaining, but when I go into the biggest cog on the back I don't seem to hear it. It also only seems to happen when under heavy load (e.g. climbing out of saddle).

I am riding an 11-spd Ultegra Di2. Chain/cassette have less than 2k miles on them and the bike is shifting well.

I can't for the life of me figure out what is going on. Any insights would be much appreciated!