rasterio.mask.mask returns a two element tuple - element 0 is the array, element 1 is the transform. Try something like (untested):
# Mask Raster
masked_raster, transform = rasterio.mask.mask(file, poly, crop=True, filled=True, invert=False)
with rasterio.open('/data/my_output.tif', 'w',
driver='GTiff',
height=masked_raster.shape[1],
width=masked_raster.shape[2],
count=1,
dtype=rasterio.ubyte,
crs=file.crs,
transform=transform
) as outfile:
outfile.write(masked_raster, indexes=1)
