If you didn't file then the IRS does a quick simple return for you to see if you should have filed a return so they know if they need to send out a bill for the unpaid taxes. When they complete your return they do not take into consideration any adjustments, dependents, itemized deductions or credits you may be eligible for ... in other words the return is not completed in your favor. So yes, it would dispute their findings to reduce taxes & penalties they say you owe.
Also you can amend to correct the carryover amounts for some items like depreciation or an NOL.
