No, it is not common practice.
Generaly a 3 months D-Visa is issued (see 18.104.22.168) in cases when issued with the goal of recieving a residence permit.
Exceptions can, however, be made (see 22.214.171.124).
In your case, since a semester generally starts in September, they probably want you to complete the process before the semester begins.
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It depends on the type of Schengen visa you have: a two-entry or multiple-entry visa would exempt you from the visa requirement in Croatia, a single-entry visa does not.
If you were a resident in the Schengen area (holding a national long-stay or “type D“ visa or a residence permit), you would also be exempted from the visa requirement in Croatia.