Absolutely. I'm not very good at finding information in scientific papers, but here's the first few I found with Google. If those don't satisfy you, I'll see what I can find when I get home from work.
http://www.ldeo.columbia.edu/res/fac/trl/downloads/Publicati... (PDF) is a paper that specifically addresses a lot of the concerns about temperature prediction using tree rings. In particular, I'd like to quote the following section as it pertains directly to your question:
"A number of tree-ring series indicate a divergence between tree growth and temperature at some northern sites in recent decades (e.g. Briffa et al. 1995, Jacoby and D'Arrigo 1995, Briffa et al. 1998, Vaganov et al. 1999, Barber et al. 2000). Theories for the cause (s) of this observed divergence, which may vary from site to site, include decreased temperature sensitivity due to warmer temperatures, drought stress, increased winter snowmelt and ozone effects. This divergence needs to be considered to avoid bias in dendroclimatic reconstructions; however it is not present everywhere. For example, temperature-sensitive elevational treeline sites in Mongolia and the European Alps exhibit dramatic growth increases in recent decades (D'Arrigo et al. 2001, Buntgen et al. 2005)."
http://www.ldeo.columbia.edu/res/fac/trl/downloads/Publicati... (PDF) is an earlier paper referenced in the above that also discusses the problem.
http://icecap.us/images/uploads/Loehle_Divergence_CC.pdf (PDF) is a paper by someone that's more skeptical, it goes into a fair bit of detail about the possible causes, mostly to argue against them.
Of course, we're getting a bit away from the actual topic. We know about the post-1960ish divergence. We know that it's a good idea to exclude that data from any kind of analysis, which isn't a problem because we have accurate modern measurements from that period to use instead. There may be other periods of inaccuracy - but if there are, they haven't been discovered, and there is a substantial amount of overlap between these reconstructions and our actual instrumental record during the calibration period. In other words, it's the best reconstruction we have at the moment, and like any scientific theory, it's subject to change if better evidence were to come along. Unfortunately, the skeptics seem to be more interested in politicizing the debate rather than finding that better evidence themselves.
None of this really changes what the comment says, which was basically "Don't use this to plot past 1960, because we know that part needs corrections". I don't see an issue with that. The wording could be better, but it's a useful note to have, to make sure that the data isn't misused. I don't think it would be necessary to say "Oh yeah, the rest is just a theory, it could be wrong too" - everyone who was supposed to have access to the source knew that. It comes with the territory. The problem is when internal stuff is leaked and that territory changes - a random person reads that comment, completely misses the tentative scientific context and thinks that the programmer is asserting the absolute correctness of everything he doesn't single out as wrong.
Edited to add in a (PDF) tag that I forgot.
