I am asked to Check This Entry on "MA Form 1: Tax-Exempt Pension should not be entered directly ...." It transferred from Federal and is correct, I don't know how to fix.

To enter your exempt State employee pension, you will first have to enter the necessary information in your Federal Income tax return and then in the State income tax return.   Here are full instructions.  Start with #6 since you've already done the 1099 part.

On the  Federal Income Tax  portion:

1. In the search or find box, type in 1099-R
2. Click on Jump to 1099-R
3. Scroll down to Retirement Plans and Social Security
4. At IRA,401(k), Pension Plan Withdrawals (1099-R), click Start (or Update)
5. Enter your 1099-R or if you have entered it, click on Edit then Continue
6. Answer the next questions until you get to the Where Is This Distribution From? screen
7. Select the source State Employees and enter the information requested:
8. Click on Continue
9. Click on From a Qualified Plan
10. Continue answering the questions

On the State return portion: 

1. At the Changes to Federal Income page, scroll down to Received retirement income, click Start (or Update)
2. At the Retirement Distributions Summary page, click on Edit State
3. If no additional information is required, click on Continue
4. Click on Done

Here is a link to the MA state website, which discusses the taxability of MA pensions.