The concept of a harem in anime may not be fundamentally broken but it definitely has some issues, including in the unofficial genre of isekai. To begin with, the harem is rarely an organic part of the narrative -- that is, many harems are formed out of a sense of obligation from a narrative standpoint, rather than being what the story requires. They are often simply forced into the story for its own sake, and not always for innocent reasons. Just the inclusion of an obligatory harem can feel trite and stale for many anime fans today, and that's not even the worst of it.
On another level, some harems are little more than wish fulfillment for targeted audiences of isekai action anime series, such as teenage boys. There's no harm in tossing in a few attractive female characters to appeal to audiences, but when a handful are inexplicably drawn to the self-insert male lead just because, the narrative becomes transparent at best. Rarely do isekai leads like Sword Art Online's Kirito or Mochizuki Touya from In Another World With My Smartphone actually earn the affection of these girls -- it's just another level to the power fantasy scenario to match the hero's incredible combat prowess. These heroes have an overpowered spell or sword in hand with a girl on each arm, and it's rarely a good look.
In some extremes, the members of these harems are treated more like prizes or collectibles than people, which can be deeply insulting and cheapen any character. These adoring fans of the isekai lead often contribute little to the story aside from fan service and comic relief; fortunately, there are some series that buck this trend. My Next Life as a Villainess creates a more wholesome co-ed harem in a series that's all about relationships, and The Rising of the Shield Hero morphs a would-be harem into something entirely new.
