In this working paper (The Paradox of Manifestos) Ian Budge replies to some of the methodological critiques of the MARPOR/CMP/MRG manifesto projects. The paradox lies in the contrast between the positive research experience of most users of the manifesto data, and the at times rather harsh methodological critiques of manifesto data.
Unfortunately the paper is quite selective in which critiques it engages with (table 2 is rather short). The biggest issues I have come across with the data in question are a rigid coding scheme (this of course has advantages, but the data can struggle to reflect the situation on the ground adequately), and party rankings that defy common sense and expert judgements. In my view the many happy users Budge identifies are a sign of good enough data (not necessarily good data), and also of the extensive coverage of the data.
Having tried and compared different methods to measure party positions, I have serious doubts whether we’re even close to measuring party positions with precision — or do precise party positions exist at all? No, I don’t want to give up on measuring party positions, after all the different methods correlate enough to agree on the ranking of parties. We should, however, always express the precision and error in measuring party positions, not just the point estimates.
Didier Ruedin 
As a small addendum, the linked paper isn’t a good example with regard to showing errors; this wasn’t forgotten (I looked at this aspect), but left for the future to explore in full details.