There's no way this is some sort of slight against David Bowie. It's not like he's not respected in all annals. I'm guessing this has more to do with the timing of his death.
Bowie died on January 10th of last year, and there was appropriate outcry. Since, there have been many tributes to his legacy, by well-known organizations and artists. Bowie died during/before award season last year, and I think he was acknowledged sufficiently during that period.
I hear that there will be a tribute to Prince and George Michael, both huge stars who died a little more recently. Though Prince died in April, I think it's possible that because of the tragic year that had already begun - and the fact that he passed after awards season - he might not have gotten the amount of tributes that Bowie did. I wouldn't go so far as to say his death was overshadowed, but to me, Prince having a tribute at the Grammys feels fine.
Short Answer: With so many celebrities dying last year, I think it's hard to judge who should and shouldn't get posthumous honors. Feels a bit distasteful to try. Best focus on who we're honoring, not who might have been left out and for what reason. And as I said, Bowie got his honors straight away. Gaga did a big thing for him at the Grammys last year.
Note: Just realized I could've saved myself a lot of time by stating Gaga's 2016 tribute upfront. That's pretty much the entire answer.