This may indeed be true. However, we have examined this issue recently and so far did not find any such bias. For instance, data on farmland bird trends in Europe from independent sources showed that PECBMS data correctly described the decline of farmland birds in the 1980s across Europe (Voříšek et al., 2010).
Nevertheless, PECBMS results that are suspected to be biased are labelled as such in all outputs. The potential effect of such suspicious species indices on supranational indices is also routinely examined, and suspicious data are abolished.
So far, there is no other option than to use a hierarchical procedure to impute missing values in European regions.
Learn more in Methods, chapter 2.2. Combining national data into supranational outputs or chapter 4. Quality control.
See PECBMS results in detail in special reports on European trends and indicators.