Retirement tax questions

Does this also apply if you receive a lump- sum pension distribution, and a portion of it is after- tax employee contributions, reported all in one 1099-R? The pretax goes to Traditional IRA, the after tax went to a Roth IRA? Seems like a significant oversight in the instructions (or was the 1099-R prepared incorrectly by the financial inst?). Ignoring the after-tax portion correctly characterized everything as non- taxable - but does that create a problem with properly tracking the after tax funds into the Roth IRA, for the future? Thx.