As well as the MIDI CCs, the MX88 also sends Real-Time MIDI messages like MIDI Clock and Song Position, etc. - as shown on the MIDI Implementation Chart near the end of this document:
For example, MIDI Clock is roughly the equivalent of someone counting time, so that the rest of a band, ensemble or orchestra knows what tempo they should play at. There are 24 MIDI Clock messages per quarter note, so your experience of trying to record the full MIDI data stream could just be showing these other MIDI messages.
Pitch Wheels, Modulation Wheels and MIDI CCs are usually programmed so that they only send out MIDI messages when their position changes - the program looks for when a change in the measured position exceeds a threshold. It is unusual for a Pitch Wheel, Modulation Wheel or CC to send out messages all the time, and that would probably be considered to be a fault. Yamaha products have ‘hidden’ built-in test routines in their firmware that can be used for checking the correct operation of Pitch Wheels, Modulation Wheels and MIDI CCs, and a service technician could use these test routines to check that you do not have a faulty one.
However, I think that the most likely explanation is that you may be seeing some Real-Time MIDI messages, rather than a faulty controller. From the MIDI Implementation Chart, these Real-Time messages would seem to be normal and should not affect the velocity response.