I have heard/read that in some cases a marriage is forbidden on the basis of mismatching kundalis/gunas.
In some other cases it's forbidden because of caste incompatibility.
Is there any relationship at all between the two practices?
My understanding is that in the case of the caste system marriage among different castes is discouraged because some castes are deemed socially superior than others. This seems to be similar to the way marriage among different social classes is discouraged in western societies, e.g. millionaires rarely if ever marry a homeless person.
In the case of kundalis matching, the practice is based on the belief that astrological events can affect the marriage, hence certain matches are discouraged.
In the case of gunas matching, the practice seems to be based on the observation that different people have different behavioural tendencies, therefore it makes sense to discourage certain matches with undesirable people.
To me it seems that there's not relationship between them except for the fact that it's practiced by Indian people which also happen to practice Hinduism.
For that matter, it looks like none of these practices has any basis in the Hindu doctrine. They seem more like cultural practices specific to certain parts of India in which people also happen to practice Hinduism.