Always leave at least one blank pixel around your atlas cells. This saves problems with scaling and also if you use min/mag filter enabled (which it is by default). Also, if you scroll the sprite in any direction, it may use 0.5 of the adjoining pixel to achieve smooth transition.
If you just want a simple 1 colour sprite then create a sprite like this:
sp=CreateSprite(0)
SetSpriteSize(sp,10,10)
SetSpriteColor(sp,255,255,255,255)
If you really need to keep your actual image crisp and "pixelly", then you need to set the min/mag filters for that image to 0. Unfortunately, this is a command that affects the image not the sprite, so I am sure your entire atlas would have to be in either/or modes.
I have started making separate tiles lately and using the imagejoiner tool that comes with AppGameKit to generate an atlas. Sometimes I have to be careful to place only images where their purpose is suitable for atlases.
I recently went through an exercise to tile up about 8192x360 worth of scrolling backdrop. The original is 2048x90 and it was scaled x4 on the screen when rendered.
The individual frames didn't join together properly if I scaled the sprite after picking it from the atlas and after a lot of experimentation, found that I had to pre-scale the original graphics, chop them up into pieces (leaving 1 blank pixel top and bottom in this case) and "sprite" them at the x4 size.
A lot depends on the actual images and what you are using them for.