1.
The amount reported on line 4a of your 2018 Form 1040 in this case does not reflect the total amount of all Forms 1099-R that you received because of the way line 4a combines the gross amount of IRA distributions with the gross amount of pension and annuity distributions. In your case it seems that only your IRA distributions are being included on line 4a and your pension and annuity distributions have been excluded from line 4a.
The IRS has recognized that the way amounts on line 4a of 2018 Form 1040 were combined was as a problem and for 2019 has gone back to having separate lines for IRA distributions (lines 4a and 4b) and for pension distributions (lines 4c and 4d).
2.
QCDs are not reflected on Form 1099-R because the IRA custodian has insufficient information to determine if the money transferred to charity actually qualifies as a QCD, so your QCD distribution is reported the same as any regular distribution. It's your responsibility to report the QCD on your tax return based on having met the requirements for the regular distribution to be a QCD (which you apparently did since you have the "QCD" notation present).
