Palpatine might have disliked clones
The Empire had a codified policy of xenophobia. Wookies and Twi’leks were often enslaved, for example. This was definitely something promoted by the Emperor himself, and not merely the prevailing attitude:
Palpatine and his propaganda machine worked to drive that nail of
bigotry deeper by demonstrating how the old Jedi thugs and the
scumfroth rebels consisted of many more nonhumans than humans. You
could trust a human, the Empire said; aliens would always betray you.
Star Wars: Aftermath: Life Debt
It is difficult to say how much Palpatine bought into this. He was a hypocrite at best: his former apprentice Darth Maul was a Zabrak, for example. Nonetheless, it seems likely that Palpatine, being a human himself, supremely arrogant, and indeed the source of much of the Empire’s propaganda, might have believed nonhumans to be inferior.
If this were the case (or even if were not), it would not be extraordinary for him to have a similar attitude toward clones. They had short lifespans, were blindly obedient, and (according to now-Legends material) were unable to effectively wield the power of the Dark Side: all things that Palpatine was likely to despise.
The Star Destroyer that we see at the end is probably not an ordinary ship. It is transporting Palpatine and Vader to view the Death Star construction. As such, it may be a flagship or other vessel important to Palpatine. In any case, if Palpatine believed clones to be inferior, his first step would probably be ensuring that the important ships had no clones among their officers.