No, casting Animate Dead does not end Time Stop: commanding them with the bonus action does end it.
We have the same edge case under the Animate Object spell, which is solved by the Sage Advice Compendium:
Does casting animate objects during a time stop spell end the time stop?
No. Commanding the newly created creatures with your bonus action does end time stop, however.
Using the Bonus Action affects the new creatures, hence it makes you meet the requirement for ending Time Stop.