Don't report a "crash", report the error you have. Is that an array out of bounds exception? A division by zero? It can happen if sampleCount is zero: you have to test this case.
Mmm, looking at the algorithm, it is wrong: why do you loop with the while without changing i?

Perhaps something like that can work (untested):

1. int i = 1;
   
2. int sampleCount = 0;
3. float runningTotal = 0.0;
4. while (i < yVals.length-1) {
5.     if (abs(yVals[i]-yVals[i-1]) < filterThreshold) {
6.         runningTotal += yVals[i];
7.         sampleCount++;
8.     } else {
9.         if (sampleCount > 0) {
10.             float average = runningTotal/sampleCount;
11.             for (int j = 0; j < sampleCount; j++) {
12.                 filteredData[i - sampleCount + j] = average;
13.             }
14.         }
    
15.         sampleCount = 0;
16.         runningTotal = 0.0;
17.     }
18.     i++;
    
19. }

It is probably wrong but unless I am too tired, the logic should be OK and you just have to adjust some details.