Assuming that I got a residence permit card in one of the Schengen countries, and returned to my homeland (non-Schengen area) without returning the residence card (physical) in the foreign affairs office, can it be an issue when returning back to Schengen area? Like they would assume that by not returning the residence card, I would still be there (in this way, illegally), or just by leaving the Schengen area using my passport, it would be automatically considered that I have left? Thanks!
This answer assumes that by "returned to my homeland" you mean moving your place of residence there. (For a short visit to your homeland, you should keep your residence permit because you will need to show it to the officers at the border to get back into the Schengen area.)
In general, if you physically leave the Schengen area, you are not considered to be present in the Schengen area. This follows from the general principle that prohibitions against unauthorized presence refer to physical presence rather than the possession of a given document. Such matters are governed by national law, however, so the details could vary from one country to the next.
You might separately be in violation of a national law that requires the return of the residence card, if such a law exists.
Because national laws are different in each country, if you want an answer addressing the situation in a given country it would be a good idea to edit your question to indicate which country you're asking about.
With that in mind:
Can it be an issue when returning back to Schengen area?
If there is a law requiring you to return the card, then yes, not returning the card might cause a problem if you return. The problem would likely be fairly minimal because the penalty for violating such a requirement would normally be relatively small.
[Would they] assume that by not returning the residence card, I would still be there?
just by leaving the Schengen area using my passport, it would be automatically considered that I have left?
Normally, yes. You will receive an exit stamp in your passport regardless of whether you return the card.