jaye.ramseysutter ,
Echoing what @kona said, can you provide the settings and the full grades (without identifying information of course) for some students whose scores you think are being calculated incorrectly?
In the almost 5 years I've been using Canvas, I've never seen it calculate a grade wrong. I've seen other people here in the Community suggest contacting Canvas Support because it's a bug, but any one I have looked at has always been calculated correctly (granted, I'm a math teacher and can read some computer code to see what's going on so I might have an advantage over some). I have seen lots of cases where what people think should happen isn't what's happening. One of those areas is when grades are dropped, especially if the point values are not the same. Without explicitly stating that, you're implying that they are all the same when you say 25%, so that's why seeing how things are setup would help.
One way to accomplish what you're describing, is to have a single assignment group, drop 1 score, and never drop the research paper.

Then, let's say I entered these grades

Exam 3 with the gray background is the one that is dropped, even though the research paper is a lower score. That's where the "Never drop" comes in. The counted scores are 90+85+97+25=297 out of 400 points, which is 74.25%.
If the research paper is missing, then you get this:

It still drops the 75 for exam 3, but there are only 272 points out of 300, which is 90.66666... and gets rounded to 90.67%
If you have the research paper, but not the exams entered, then you might get something like this:

It still drops the exam 3 score and now you have 200/300 for 66.67%.
All of the calculations are spot on and most people have no trouble following the calculations.
Where things get tricky is if you have different point values.

Notice that they got 40/50 = 80% on Exam 1 and 75/100 = 75% on Exam 3, but Canvas drops Exam 1, not Exam 3.
Canvas does not drop the lowest percentage, it drops the grade that hurts the most, so it is correct to drop Exam 1.
- Dropping Exam 1: Exam 2 + Exam 3 + Exam 4 + Research
- Student points: 85 + 75 + 72 + 25 = 257
- Possible points: 100 + 100 + 75 + 100 = 375
- Final average = 257/375 = 68.53%
- Dropping Exam 3: Exam 1 + Exam 2 + Exam 4 + Research
- Student points: 40 + 85 + 72 + 25 = 222
- Possible points: 50 + 100 + 75 + 100 = 325
- Final average = 222/325 = 68.31%
Dropping Exam 1 results in a higher final percentage for the student (68.53% vs 68.31%), so that is the one that Canvas drops. The fact that the student did better percentage-wise on Exam 1 (80%) than Exam 3 (75%) is irrelevant and not figured into the calculations. The decision about which one to drop is based on the overall grade. You may lose the battle (drop an exam with a higher score) to win the war (end up with the higher grade).
While the above approach -- a single assignment group, drop 1 grade, never drop the research paper -- is the easiest route, there are other ways you could go. You could set up two assignment groups, one for exams and one for the research paper. Then drop one assignment from the exam group and don't drop any from the research paper group. Sorry I can't include a screenshot right now, my beta instance of Canvas has gone into maintenance mode and I want to get this message out sooner rather than later. Other people could use a weighted gradebook and if they did that, they would need to make the Exams worth 75% of the grade and the research paper worth 25% of the grade. They would still need to apply the "drop 1 lowest grade" rule.
The most common concerns about the gradebook being wrong deal with extra credit, dropping assignments, missing assignments, and weighted assignment groups. If the above doesn't explain the discrepancy, then we really will need to see what you think is a wrong calculation along with any rules (dropping grades) that you have to help.
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