Is there a known reason why people feel a bit bad after other people do something for them? There's an Thai word: kreng jai (the feeling of not wanting to disturb/inconvenience another person, or feeling uneasy due to your own request of someone) 

Likewise in Burmese the word "anade" which is "a strong sense of consideration for others' feelings and a desire not to cause them to feel psychological distress, unease, or burden" and in Japanese the similar word "enryo".

There seems to be a common cross-cultural feeling of distress at being a burden.

Is there a psychological explanation for why people feel bad instead of good, if someone were to help them with something?
What you seem to be talking about here are cultural influences affecting your judgement on what is right and wrong to say and do in certain situations.
Ecologies shape cultures, and cultures influence the development of personalities (Triandis &amp; Suh, 2002).

The conceptualization of culture is by no means a simple matter. One possible way to think about culture is that “culture is to society what memory is to individuals” (Kluckhohn 1954). It includes what has worked in the experience of a society, so that it was worth transmitting to future generations.

Triandis &amp; Suh (2002) went on to say that:

Funder (1997) defined personality as “an individual’s characteristic pattern of thought, emotion, and behavior, together with the psychological mechanisms— hidden or not—behind those patterns” (pp.1–2)

The kind of situation you talk about would not be seen as often in Western countries, but it seems to be widespread in Eastern cultures.  To use the Thai culture of เกรงใจ (Kreng Jai) you linked to in your question, as you pointed out, it is insisted that you must not cause anyone distress or discomfort.  But, Kreng Jai can be vexing and cause distress in itself as the insistence can even be

at the expense of efficiency, honesty, or one’s own interests (Thailand Family Law Center, 2012).

If you look at Fitzroy (2014), there are good aspects to Kreng Jai in business and general society.

By demonstrating more courtesy amongst the team you show more compassion and empathy which can lead to better teamwork and better results.

However, there are many ways where if Kreng Jai was over used, it can cause all sorts of problems.  For example, being too Kreng Jai to ask your boss for help can result in an important task not being completed on time.  This can cause cause loss of revenue for the business, and embarrassment for both parties.
When feeling bad for &quot;being inconsiderate towards others feelings on the matter&quot;, it can cause a lot of psychological discomfort, and this is what you are describing here.
References
Fitzroy, P. (2014). เกรงใจ (Kreng Jai) – overused or misunderstood? Retrieved from: https://www.linkedin.com/pulse/20141015014001-50338470-%E0%B9%80%E0%B8%81%E0%B8%A3%E0%B8%87%E0%B9%83%E0%B8%88-kreng-jai-overused-or-misunderstood
Funder D. (1997). The Personality Puzzle. New York, NY: Norton
Kluckhohn, C. (1954). Culture and behavior. In Handbook of Social Psychology, ed. G Lindzey, 2:921–76. Cambridge, MA: Addison-Wesley
Thailand Family Law Center. (2012). Demystifying Kreng Jai. Retrieved from: http://www.thailand-family-law-center.com/demystifying-kreng-jai/
Triandis, H. C., &amp; Suh, E. M. (2002). Cultural influences on personality. Annual review of psychology, 53(1), 133-160. doi: 10.1146/annurev.psych.53.100901.135200