Proteins would also react to FCR. During extraction usually methanol/ ethanol precipitation does the job. Xenobiotic aromatic compounds, or chemical reagents/ artifacts from  different extraction matrices may give false readings. Tough to control everything. So, HPLC-based identification and quantification is more trust-worthy than FCR-based spectrophotometric assays. best wishes. 

MANY things, which is why it is increasingly contested and not sufficient for publication in many leading journals. Proteins, many reductants including ascorbic acid, sometimes sugars etc. Also the various phenolic compounds have differneing responses in the Folin-Ciocalteu assay, so the standard needs to be clearly state (there are 2 schools about that: chose a predominant polyphenol from the sample or gallic acid for comparison's sake). Here is a publication where authors measure Folin-Ciocalteu response before and after polyphenol binding on a C18- column in solid-phase extraction  to correct for interfering substances: J Agric Food Chem 53 (2005) 1370 ,  DOI: 10.1021/jf048396b (but it becomes quite time-consuming, so taking the time to identify the phenolic compounds and establish calibrations on HPLC can really be worthwhile, and as Biswapriya Biswavas Misra wrote earlier, this is the real thing).

Thank you very much dear Renard and Misra for your informative answers 

Catherine M G C Renard is right, the Folin-Ciocalteu assay is useless to determine the total polyphenols, since does not reflect the total phenolic content. I am afraid, that the removing of interfering substances can take more time, reagents, effort and etc., than performing the HPLC analysis.

However, the Folin–Ciocalteu could be used to measure the sample reducing capacity.

I think that those publications can help:

http://www.sciencedirect.com/science/article/pii/0043135483901112

http://pubs.acs.org/doi/abs/10.1021/jf030723c

http://www.sciencedirect.com/science/article/pii/S0926669014003331

Thank you Mr Paweł Górnaś

Ascorbic acid interfers depending on the concentration. Other reductant subtances such as sodium metabisulphite and L-cysteine may also interfer.