I have French Schengen visa (type D, study in France for 5 months) and Finnish Schengen visa (type C) and Russian citizenship. I took a coach from Russia to Finland and flight from Finland to France. I informed passport control that I am going to study in France, but they stamped Schengen type C anyway. On the national French Schengen there is no stamp about entry, it turns out that by the end of my studies I "will stay" in type C for more than 90 days. Is it okay, and what do I do with my documents? Or who/where should I go/call/write to for official information about it (OFII, Embassy or anything)?
The Schengen system does not work like some other systems where you are admitted in a particular status. The stamp only says that you entered (or left) on a specific date in a specific place.
The D visa essentially supersedes the C visa. For example, while you have a valid D visa, the days you spend in the country that issued the visa do not count toward the 90/180 calculation that applies for your C visa.
This is covered in the Schengen Borders Code in the second paragraph of Article 6, the last sentence of which says:
Periods of stay authorised under a residence permit or a long-stay visa shall not be taken into account in the calculation of the duration of stay on the territory of the Member States.
In principle, the stamps should go on another page, ideally next to the visa (not on it) but ultimately it doesn't matter. The border guards are not stamping one visa or the other, they only document the fact that you were granted entry and crossed the border at a particular border post at a particular time.
That stamp should be enough to satisfy OFII of your date of entry if the issue comes up at all. Meanwhile, having a valid D visa covering the period should be enough to avoid any trouble when leaving the Schengen area.