As well as the "wolf note" effect (short duration, "thuddy" notes that others have mentioned) there is also a frequency shift effect. When two resonators of similar resonant frequency couple strongly, the resonances tend to "repel" each other. So a string trying to play G at 98Hz and a guitar box with a main air resonance at, say, 99Hz will result in the string playing at a lower frequency on that fret compared to the 98Hz it should be sounding at. This type of over-coupling problem can result in local intonation errors on the fretboad of + or - 30 cents, depending on whether the played note is higher or lower in frequency than a nearby body resonance. This level or error is more than audible and is why some guitars seem impossible to tune. The more responsive the guitar, the bigger the problem. The fix is the accurate placement of body resonances between scale tones and making the "geometric" intonation as accurate as possible so that errors don't aggregate, but there is nearly always some degree of residual intonation error due to over-coupling. It is up to the builder to place these and minimise them so they cause least offense and reduce the player's effort required to push or pull a note into tune.
Trevor Gore: Classical Guitar Design and Build