The message you quote in your title is normal and not a cause for concern. I get a similar message in the code below. Is there a problem with the result of your code?
library(dplyr)
DF <- data.frame(G = c("A", "A", "A", "A", "B", "B", "B", "B"),
G2 = c("X", "X", "Y", "Y", "X", "X", "Y", "Y"),
Val = 1:8)
DF |> group_by(G, G2) |> summarize(S = sum(Val))
`summarise()` has grouped output by 'G'. You can override using the `.groups` argument.
# A tibble: 4 x 3
# Groups: G [2]
G G2 S
<chr> <chr> <int>
1 A X 3
2 A Y 7
3 B X 11
4 B Y 15