Taking means using two criteria for the group_by argument

You are mixing base R with tidyverse syntax here, when working with tidyverse functions there is no need for JS_CU$ before the variable name. I can't test this because you are not providing a REPRoducible EXample (reprex) but I think your code should be like this:

JS_CU %>% 
  group_by(time_int, survey) %>% 
  summarise(mass_mean = mean(mass, na.rm = TRUE))
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