Issues with Eraser Function

I am using the Development version of Inkscape.

I have an image of a fish, with no scales so in order to create them I have to do it in a round about way.I have used the clone function to help me create scales on a fish. This is what I did

Made 3 layers
Top original image (also where the final scales will appear)
Middle, scale "template"
Bottom, background

Used the Clone Tile function, using a circle as the image to clone, and then moved these tiles into place as needed.

The image is black on a white background. To make it easier I did my template in red, so I could easily see and erase parts I don't need. This is where my problem occurs. I tried to erase the excess parts of the tiles, but nothing would erase. I made sure I was on the right layer, mad sure the tile I wanted to partially erase was selected and still nothing happens when I use the Cut From Objects function. The other erase function works though. (on a side note, I'm still baffled why it works as a delete function). The Cut From Objects function does work in the top layer, though. Does this have something to do with the fact that I'm erasing something red?