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As a follow-up to the previous comments, you raise certain issues which are important and need further clarification which is probably beyond the scope of the advice we can provide.  Whether you were truly an independent contractor versus an employee is a question of fact.  As the IRS has previously stated,  

"In determining whether the person providing service is an employee or an independent contractor, all information that provides evidence of the degree of control and independence must be considered....There is no “magic” or set number of factors that “makes” the worker an employee or an independent contractor and no one factor stands alone in making this determination. Also, factors which are relevant in one situation may not be relevant in another."

Here is the link to the IRS webpage from which the above quoted information was obtained.

Independent Contractor or Employee

A very important factor in determining whether you were an employee versus an independent contractor is the level of control the company had over you and the work you performed.  In this regard, the IRS has stated,

"Under common-law rules, anyone who performs services for you is your employee if you can control what will be done and how it will be done. This is so even when you give the employee freedom of action. What matters is that you have the right to control the details of how the services are performed."

Employee (Common Law Employee)

Lastly, leaving aside the independent contractor/employee issue, you did receive ISOs and whether that was correct or not, the fact remains that is what you have.  Treating them as if they were NQSO, while that may appear to be the safer option, may not be consistent with the company's incentive compensation plans and whatever agreements/contracts they have in place with respect to their ISOs and NQSOs (assuming they even offer NQSOs).  Thus, in addition to what you have stated, you may need to discuss the matter with the company.  

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