Yes. It’s intentional that when you filter notes, tuplets remain selected - this is a necessity if you were planning on copying and pasting those notes elsewhere, as you’d almost definitely want to copy the tuplets as well as the notes.
For deletion, you’d need to Filter Lowest/Highest, then set Filter to Deselect, then Filter Tuplets. Then delete. It’s worth assigning key commands for all of these things, or possibly even recording a script (or building a macro with third-party software) if this is something you do a lot.
The other approach is to select a note and then use Select More (Cmd-Shift-A or Ctrl-Shift-A) a couple of times, to select more notes. When you then Filter the lowest/highest note, the tuplet won’t be selected, because you hadn’t selected it in the first place.