I had this problem with my 1996 civic before. With an warm engine, shifting from 2 to 3 causes the engine to rev very high for fraction of a second. I took it to a Honda dealer and they said "Transmission has a flare". They asked me to replace the transmission.
Then I took it to Aamco and they said linear shift solenoid need to be replaced. It was replaced and the problem recurred in 3 months. I asked them to go for Honda parts this time. They did that (as they said). Again after 1 year the same problem.
It has 228K km, coolant level is okay, Transmission fluid is OK (changed a year ago and its pink), regularly changing oils from Honda dealership.
I know it will cost me another 400 dollars to replace the solenoid. Any idea why its going bad so frequently? Thanks.