That is a known issue according to the release notes of Core21 v0.0.18 and should be fixed in the next release v0.0.19, but it's now a few weeks later and I have not seen a new Core21 version yet. It should not affect the WU, see:
- New Core21 v0.0.18 with NVIDIA bug workaround released!
 

by JohnChodera (Pande Group Member) » Mon Jan 30, 2017
 
We are pleased to announce the release of Core 21 v0.0.18 to full FAH.
 
This release contains a workaround for a change made in the NVIDIA OpenCL driver introduced in drivers starting with 375.57, as well as some improvements to error handling codes.
 
While a slight reduction in performance may be observed, this performance regression should be eliminated when NVIDIA removes the hotfix in forthcoming driver updates.
 
There is a known issue that this release will, for some projects, print sporadic messages to the log due to a known visualizer bug:
 
05:34:52:WARNING:FS01:Size of positions 64914 does not match topology 19
 
This issue does not affect the quality of the science, and a workaround is already in testing for v0.0.19, which we hope to release in a week.
 
Thank you all for your patience.
 
~ The FAH Core 21 crew

There is just an update posted by JohnChodera on the Folding Forum, see:
- New core21 0.0.18 with NVIDIA bug workaround released! [Update]

by JohnChodera » Mon Mar 27, 2017
 
UPDATE: NVIDIA win driver 378.66 should be the first version where the NVIDIA FAH hotfix has been removed.
 
We have a test build of 0.0.20---which fixes the visualizer problems---in testing right now.
 
Thanks for your patience!
 
~ The FAH Core 21 crew

This has been happening for quite some time. It doesn’t affect anything. I just ignore that warning.

Seems like topology errors occur when overclocking too close to the maximum. 
On RTX cards the threshold is around 90Mhz overclock on GPU.
Some cards go up to 99Mhz, some start failing at 59Mhz (depending on how hot they run, and if you have a good or bad bin GPU chip).
If the error is occurring and you overclock any faster, errors occur and batches fail.
Usually clocking them between 1 to 5Mhz slower, will get rid of these errors.
On some cards I run a 87Mhz overclock for that reason, as the 92Mhz the other cards can do, doesn't work for these cards.
 
 
edit Cool GTX, PM sent

All 9 of my cards are running stock, same error across the board, still no issue. I do notice it in the logs a bit less at times but kinda thought it may be different WU's. As it never presented an issue to ppd, I haven't bothered putting it in my list of things to do. Mainly because that list is long enough.

I see more of them at higher overclocks.
Running them at lower overclocks I see less or none.
On my RTX cards, anything past 90-95Mhz overclock will show a whole bunch of them.
Once they are showing, they will continue to show until the WU is finished. Even if you only have 1 error, it'll keep posting for the entirety of the WU.

Likewise, you can have a wu without any topology errors, and somewhere after a few percent, crank the overclock to ~90-100Mhz (whatever is specific to the card) and start seeing floods of topology errors.