What about these?
The animal was classified in that category, because people had a hard time classifying it, but that category made the most sense for most world-renown experts at that time, before it was put in a different category.
The animal was classified in that category, because people had a hard time classifying it, which was because of the lack of categories at that time, but that category made the most sense for most world-renown experts at that time, before it was put in a different category.
That's a bit better, but do you mean this The animal was classified in that category. . before it was put in a different category.
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That's a bit better, but do you mean this
The animal was classified in that category. . . before it was put in a different category.
or do you mean this?
. . . but that category made the most sense . . . before it was put in a different category.
You need to make it easier for the reader to follow your meaning. The simplest way to do that is to break