NR9R pisze:

...gave up after experiencing too many issues. My first 5000D was an early 2010 model. It was received with the misprinted label and QSK issue. I also had an issue with RF feedback sneaking into the headphone jack that required multiple trips to Yaesu to fix. Since this one felt like a lemon I returned it.

My second 5000D purchased in 2012 developed the OLED failure. Then the internal antenna tuner failed the first time I used it. After getting it fixed I sold it and decided to take a break from the 5000.

Both 5000Ds that I owned showed slight but noticeable receive audio distortion when both receivers where engaged as if the audio amp became overloaded. This is known by many owners and a general work around is to use an external audio mixer to drive the speakers and headphone.

NC0B did some measurements of the transmitter IMD and showed that with the processor engaged the IMD performance falls similar to 12V transistors, even in class A.

Another issue that seems to be increasing in frequency is failure of the VFO-A digital encoder. This has been reported by several owners on the FTDX-5000 Yahoo group.
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In my case I decided to move (down) to the FTDX-3000D. It has a similarly nice sounding receiver and if it ever develops a problem it won't be an issue to ship (the 5000D costs $150 to ship one way).

VE6TL pisze:

Other problems I've had with the rig include:
1) S-Meter occasionally sticking to the left pin (which is always fixed with a slap to the left side of the radio).
2) Vertical line (one or two of them) randomly appearing on the VFO-A OLED display. This initially went away with the firmware upgrade but came back a few months later. It seems to come and go and doesn't really affect the operation of the rig.
3) VFO-A rotary encoder very noisy. Apart from the main tuning knob, this is the second most used control on the radio. It controls the filter selection, notch, APF, DNR, IF-Shift, VRF, clarifier frequency, etc. Turning the knob one way or the other often results in random settings. Other FT5000 owners have also reported similar results with theirs, with one having opened up his rig and finding a "cheap and poor quality" rotary encoder.
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4) The station monitor is pretty useless, so I've been using a third party pan adapter which has made a huge improvement on "seeing" the signals.