BessyK I haven't noticed that happening in normal circumstances, but I have noticed that if I accidentally recommend a comment which I already recommended earlier (especially if it's on a different device or if I went out of the article and then came back in later and forgot which comments I already liked), it will show briefly as recommended but then remove the recommendation and drop the number of "likes". So it basically takes it as removing the original recommendation. If I re-like it again after that (or like a comment I didn't already like) then it stays, though. Could that be what you're experiencing?
I am prepared to give the Times the benefit of the doubt on this, as they have been producing so many excellent GC articles and comments over a long period - commentators such as SilverLady usually have great contributions, and they are allowed to stand even if they would be considered very "controversial" by some other publications.