No, it is not true that you don't have to file your 1099-...

I am trying to input a 1099-R for military retirement and it shows up in Turbo Tax as a penalty for removing money from a pension account.

I have heard if you are a disabled veteran you do not have to file the 1099-R. Is that true?

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No, it is not true that you don't have to file your 1099-R if you are disabled. The IRS requires that 1099-R distributions be reported however you may be exempt from the penalty due to disability. A disability exemption applies to the total and permanent disability of the plan owner. See IRS Retirement Topics - Exceptions to Tax on Early Distributions.