This may be old, but first for me.

Was making a reservation online for a Saturday to Saturday reservation.
Marriott.com shows a breakfast package of XXX. Rate rules says room + breakfast included. No mention of weekend only or whatnot. There is however a "rate change" starting Monday night through Wednesday night for a little bit more. I'm okay with a rate change.

After making the reservation, I see on the reservation email that it is actually:

Saturday to Sunday (Stay for Breakfast): XXX
Monday to Wednesday (Best Available Rate): YYY
Thursday to Friday (Stay for Breakfast): ZZZ

Maybe I was naive to think the rate change is a "change in the $$$ rate" and not a change in the "rate plan" and no breakfast is included for part of the stay.

Anyone else experience this?

No, not without booking back-to-back reservations myself. I have booked back-to-back reservations where one includes breakfast and the other does not.

Often when booking stays that span weekdays and weekends, Marriott reservation engine has routinely given me the higher rate for Thursday evenings so I have routinely booked (for example) a Tuesday-Sunday reservation as two separate stays, the first being Tuesday-Thursday and the second being Thursday-Sunday resulting in the Thursday night rate almost always being lower this way. It appears that their booking engine has given you the lower Thursday rate, which has not been the case IME. Now is this a one off, or did they fix this shortcoming of their booking engine? I would still recommend checking prices for the Thursday-Saturday portion of your reservation. You still may find booking back-to-back reservations may be a better deal.

Note: in your post you said your reservation was Sat-Sat, yet where you detail your stay the last portion indicates it is Thursday-Friday? Are you staying Sat-Sat or Sat-Fri? I assume where you wrote Thursday-Friday that you really meant Thursday-Saturday when formulating my response above.

I've done back to backs as well, but the rate change is consistent with booking it separately (higher during monday to wednesday nights). That is why when I booked it I thought it would be cheaper to book it straight through with breakfast.

I am actually staying Sat to Sat. I listed it for the "night of":
Sat and Sunday night 2 nights Stay for Breakfast Rate
Monday to Wednesday night 3 night Best Available Rate
Thursday to Friday night 2 night Best Available Rate (rate lower than M-W)

Agreed. Many times I have to dink around with the arrival/departure dates and end up with two or three back to backs because the rate is better for a couple of days and not the others. Use the flexible dates search option to see the calendar and then change number of nights to get best rates.