ggplot2 error : Discrete value supplied to continuous scale

Now that we know the two color vars are of different types, there's the issue. You can try using a different scale for one (e.g. fill instead of color)

set.seed(123)
my_df1 <- data.frame(a=rnorm(100), b=runif(100), c=rep(1:10, 10))
my_df2 <- data.frame(a=rnorm(100), b=runif(100), c=factor(rep(LETTERS[1:5], 20)))
 
# this won't work. can't assign discrete and continuous to same scale
ggplot() +
  geom_point(data=my_df1, aes(x=a, y=b, color=c)) +
  geom_polygon(data=my_df2, aes(x=a, y=b, color=c), alpha=0.5)

Error: Discrete value supplied to continuous scale

# but use fill for polygons, and that works:
ggplot() +
  geom_point(data=my_df1, aes(x=a, y=b, color=c)) +
  geom_polygon(data=my_df2, aes(x=a, y=b, fill=c), alpha=0.5)

If you have to use the same scale (color), and can't convert the variables to the same type, see this for more info: Plotting continuous and discrete series in ggplot with facet

Evidently, you can't have different color aesthetics for two different geoms. As a workaround, use a fill aesthetic for the points instead. This means you have to use a point marker style that has a filled interior (see ?pch and scroll down for the available point styles). Here's a way to do that:

ggplot() + 
  geom_point(data=merged,aes(x = pauseMedian, y = numTotalPauses, fill = diff),
             pch=21, size=5, colour=NA) +
  geom_polygon(data = splineHull, 
               mapping=aes(x=pauseMedian, 
                           y=numTotalPauses, 
                           colour = microstyle),
               alpha=0) 

Adding colour=NA (outside of aes()), gets rid of the default black border around the point markers. If you want a colored border around the points, just change colour=NA to whatever colour you prefer.

Also see this thread from the ggplot2 Google group, discussing a similar problem and some workarounds.