No, Trump did not question the number of people who died. He questioned the fake statistics used to multiply the official death toll by about 50 fold.
As a brief reminder the report written mainly by SJWs at GWU used an unsupported estimate of the number of people who allegedly left the island in the months after the hurricane. There were 16,608 deaths in the sixth months following the hurricane. The report estimates that there should have only been 13,633 deaths. That's because they assumed the correctness of an estimate of 3,327,917 total population before MAria and an estimate of 3,048,173 afer Maria. Those are both unsupported estimates especially the latter which was based on surveys of airline passengers about whether they were leaving and not coming back.
Figures never lie, but liars figure. Expecially ComDem Liars.