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In your yAxes config you set stacked: true
this means for the first dataset it takes 0 as the bottom but for your second dataset it takes the first dataset as the bottom. So if the 2 datasets have 10 and 5 as first datapoint the first dataset will draw it at 10 and the second one will draw 5 above it at 15.
To solve this issue you will need to remove stacked: true
from your config like so:
yAxes: [{
ticks: {
min: 0,
stepSize: step,
fontColor: "#300",
fontSize: 14
},
gridLines: {
color: "#000",
lineWidth: 2,
zeroLineColor: "#000",
zeroLineWidth: 2
}
}],
Source:stackexchange.com