Limitations of opportunity cost:

The concept will not be applicable on those factors of production which are fixed in supply and whose use is specific and have no alternative use. Thus, their opportunity cost will be zero because they do not have alternative uses.
 
The concept assumes the perfect mobility of the factors, but ,t is not true because many non-economic factors like religion, language, Caste, etc do not make the factors fully mobile. If factors are immobile, then their prices do not reflect opportunity' cost because their use does not impose sacrifice.
 
The assumption of the concept that all the factors of production are
homogeneous is also not true. In fact most of the factors are heterogeneous these days. All labourers are not alike some may be more skilled, others less skilled and still others quite unskilled.
 
Its assumption of perfect competition is also not true. What prevails in real life is the monopolistic competition.
 
To calculate accurate opportunity cost is a very difficult job. Sometimes the alternatives foregone cannot easily be established e.g. the acquisition of a durable capital asset which may not have opportunity cost over the time its use is spread. Thus, it is only an imaginary cost
 
It is difficult to establish the difference between individual and social cost.
 
It is difficult to ascertain the opportunity in terms of social sacrifice.