As far as the Covered California application, using their income on the application may or may not have hurt. The Credit is based on the household income, and the members of your family so if you would have claimed them, your credit should have been spot on. However, many people are in your exact situation- a year ago you intended to claim them as dependents but they are at the "between" stage so as long as you did not do it fraudulently. The allocation allows you split off both the income and the credit so it would be "as if" the policies would have been separate to begin with.
It may be to your advantage to look at allocating some of the amounts to the stepsons (you may find after entering the information you owe some of the subsidy back)- regardless because they are on your 1095-A they will each also have to report the 1095-A even if you choose not to allocate any of the amounts to them. Read the article below and post again if you have more questions.
What is Form 1095-A: Health Insurance ... - TurboTax
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