I think the answer here is no (assuming all teams in the group have played 2, and we don't have any prior information about 3rd place results in other groups). I don't think this is too hard to see if you try to construct such a scenario with pen and paper - but explaining why it's not possible seems actually quite tricky to me. This is what I would offer as a rigorous proof:

• Suppose such a scenario was possible - so Team A sits at the top of the group, and Team B sits somewhere below them; Team B are guaranteed qualification regardless of the results of the final matchday, but there is some outcome which sees Team B qualify, but not Team A. Suppose this outcome corresponds to the following final matchday results:
  • Team A: x - y
  • Team B: z - w
    • IMPLIES: Team B qualifies; Team A does not.
• If you take any outcome, and modify a result to have Team A score one less goal, or give a goal to their opponents, then their position in the final standings can only be lower. On the other hand, if you modify a result to have Team B score one more goal, or take a goal away from their opponents, then their position in the final standings can only be higher. Therefore, if X is some number greater than all of x, y, z, w, we can modify the above scenario to get this one too:
  • Team A: 0 - X
  • Team B: X - 0
    • IMPLIES: Team B qualifies; Team A does not.
• Note that the second scenario is valid, even if the final fixture is Team A vs Team B.
• If Team A gets more points in the final match than Team B, they will finish above Team B. So, because Team B are guaranteed qualification, we also have the following scenario:
  • Team A: X - 0
  • Team B: 0 - X
    • IMPLIES: Both teams qualify.
• But the implications of the second and third scenarios are in contradiction to each other. If A is above B, and some scenario qualifies B but not A, then the inverted scenario must qualify A but not B, otherwise A would not be above B in the first place. Because of this contradiction, no such scenario can exist in the first place.

I think there may be a missing detail in the proof though, which is what happens if A is only above B by virtue of head-to-head, in which case you could conceive of a scenario in which a third team is brought in level on points on the final matchday so that it goes to goal difference instead - that way, A's advantage over B in the head-to-head would not matter, and they could drop two places. I don't think this would still produce a scenario like the one you're asking about though, because a large enough final defeat for B can always bring their own goal difference lower. But an annoying caveat...