Whether or not a contractor is entitled to additional money at the end of a project is entirely a function of the way the contract is written. Unfortunately, homeowner contracts are often short form, rarely cover complex issues such as change orders adequately, and often do not even fully describe the scope of work.
Even in the commercial/industrial world I live in, disputes over extra compensation are common, in fact I can't remember a project I have worked on where there wasn't at least one request for extra compensation by the contractor. The difference between commercial projects and residential projects is that the contracts for commercial jobs are typically very thorough, are reviewed by an attorney on both sides, and are typically based on well developed model contracts where the meaning of all the words has been carefully thought out, the scope is usually pretty clear, and the commercial terms and conditions have been litigated to death, so both sides usually know pretty well what they are in for. Even so, disputes over costs are common.
There are many potential legitimate reasons why a commercial contractor may be entitled to extra money, even on a "fixed price" or lump sum contract. For example, if the Owner requests additional services, that is always grounds for extra compensation. If differing site conditions are encountered that requires extra time or materials, extra compensation is usually in order. If there is an increase in cost of commodities such as fuel or copper, that may be legitimate grounds for cost increase. Acts of God such as flood, fire, tornado, earthquake etc. that damage equipment or make the site inaccessible may be grounds for increased cost. Force Majeure (this means actions that impact a project beyond the control of the contractor such as a strike delaying shipment of equipment or materials) may be grounds for extra compensation. There are many other possible reasons for legitimate extra costs, for example defective plans, material shortage, defective specifications, inconsistency between plans and specs, and a variety of less common issues.
The point of all this is that without reading and understanding the contract, it is impossible to make any meaningful statement about whether a contractor is entitled to additional compensation on any project. The problem is made worse if the contract is incomplete, poorly worded, difficult to understand, or unusual.