If you change 1 range you have to change the others to match, i.e. for counting up to row 1000 try

=COUNTIFS(Tracker!$I5:$I1000,DATE(YEAR(TODAY()),MONTH(TODAY()),1),Tracker!$F5:$F1000,">11:30",Tracker!$F5:$F1000,"<12:00")

Note that this part

DATE(YEAR(TODAY()),MONTH(TODAY()),1)

could be shortened to

=EOMONTH(TODAY(),-1)+1