Hello - when you paste something into Atto from outside of Moodle, you may want to first paste your content into a program like TextWrangler or JumpCut so it can ensure any excess code is stripped out. If you paste something into Atto, click on the HTML icon and see if you see any strange code (before you save the page) that you did not intend to add. Atto has a PasteSpecial plug in that I've used. it doesnt strip everything out, but it does catch some things.
Then... then there is the issue where everything looks fine but as soon as I go back into edit mode of the activity, Atto has injected many things. For that scenario I've created a tracker in case you have any additional things to share: https://tracker.moodle.org/browse/MDL-63365