Many metathesis reactions with ruthenium catalysts are hampered by unwanted isomerization of the newly formed double bond, and it is believed that ruthenium hydrides that form as a side reaction are responsible. In one study  it was found that isomerization is suppressed in the RCM reaction of diallyl ether with specific additives capable of removing these hydrides. Without an additive, the reaction product is 2,3-dihydrofuran and not the expected 2,5-dihydrofuran (together with the formation of ethylene gas). Radical scavengers, such as TEMPO or phenol, do not suppress isomerization; however, additives such as 1,4-benzoquinone or acetic acid successfully prevent unwanted isomerization. Both additives are able to oxidize the ruthenium hydrides which may explain their behavior.
Another common problem associated with RCM is the risk of catalyst degradation due to the high dilution required for some cyclizations. High dilution is also a limiting factor in industrial applications due to the large amount of waste generated from large-scale reactions at a low concentration. Efforts have been made to increase reaction concentration without compromising selectivity.