Yes especially in case of some plants like Castor and Jatropha biodiesel , the layer of ester and glycerol is very difficult to separate .

This problem can be observed mainly if the conversion is not complete yet. The mono and diglycerides contains polar parts as glycerol and apolar parts as alkylesters, therefreo formally act as "phase-transfers" betwene the glycerol and FAME phase.

Yes, any one may face difficlties in separation as both types of compds. are high Boiling and having neutral functionality

The separation is the most difficult step. Presence of other impurities such some solid impurities and excess methanol makes the process more difficult. Solid impurities may cause the formation of emulsion, excess methanol will lower the interficial intension between the two liquids which leads to more difficult separation. Centrifugation or gravity separation would become difficult. It is therefore necessary to use minimum methanol with separation at low temperature and filtering before separation. In case of more difficulty it is better to introduce a coalescer system.