Hey, I am seeing the same issue. There is another thread on this forum discussing similar issues.
In my case, part way through the ESPP Step-by-Step, the screen starts saying "shares from Not employer stock".
When you click "Yes" on the "Was this a sale of employee stock?" screen, it creates a worksheet to calculate the adjustments. But, halfway through the process, once you click "Continue" on the OK, we just need a few more details" screen, TT creates another worksheet that is not actually properly connected to the transaction (that seems to be the bug). So you end up with 2 partially filled out worksheets after the whole process, and so TT can't calculate the proper compensation income to do the cost basis adjustment.
Here is the what I found as a work around. I switch between the Step-by-Step view and the Forms view.
Initially populate the share sale data from 1099-B in Step-by-Step view.
When you get to the the Tell us about the ESPP sale screen, select the employer, click next. It brings you to the "OK, we just need a few more details" screen. Switch into the form view (from that point on don't use the Step-by-step interface for the sale). Manually fill out the Employee Stock Transaction Worksheet with data from your form 3922 for this particular transaction. You should scroll down a little bit and confirm you see the correct Compensation Income in that sheet once you fill out the info.
Switch back to Step-by-Step view. Click on some tab like "Personal Info" (so that you don't proceed through the Step-by-Step for the transaction. Then you can go again to the Federal Taxes/Stock Sales/brokerage screen, "Edit" the transaction you just entered, click through "Next/Done/Continue" (without changing any of the data), until you get to the screen where it says "Here are the ESPP purchase lots we have so far", and it should have the correct info associated with that sale. At least this convoluted process works for me.
Now repeat the process for the next ESPP sale.
