25% is the subject and population the object of the preposition of.
Fractions and portions can be singular or plural depending of the object of the preposition following.
In the sentence, population is the object of the preposition of. The question is that population is a collective noun and singular, although sometimes functioning as plural (for instance, when referring to all the persons inhabiting a country or region).
Collective nouns can be either singular or plural depending on the verb used by the author to refer to a singular entity or a plurality of members.
In this case, there is no such a specification, so I consider that up to 90% of Indian population suffers from Vitamin D deficiency.
I agree with you. That fits with the rule I have always known. With portions, fractions, percentages of something, the object of the preposition determines the number of the verb. This an exception to the "don't choose verbs based on prepositional phrases" rule.
Examples:
1a. Half of the cake is missing.
1b. Half of the cakes are missing.
2a. Some of the pie was eaten.
2b. Some of the pies were eaten.
3a. Most of the beer was consumed.
3b. Most of the beers were consumed.
4a. Up to 90% of the Indian population suffers from vitamin D deficiency.
4b. Up to 90% of Indian people suffer from vitamin D deficiency.
See the rules here (specifically rule 9):
Subject and Verb Agreement | Grammar Rules