Some of AA issues and remedies...

CSS related Issues
a). If the body element has a class attribute then the class is moved from body to the enclosing div tag.
If the style is applied directly to the body element then it is not transferred. causing some issues in the page layout.
Ex: xxx.css

This will cause the menus and outline tree nodes to render with text aligned center.

b). Similar to the above I have seen some clients applying styles to the form elements directly, that caused the search box form elements to render improperly.
c). We overlay certain elements in AA on top of the page content, better to avoid adding higher z order to the elements.

Workaround for above: Do not apply styles on elements rather than create classes and apply the classes to the form elements.

Note: This is fixed in 6.6 Mako.

Template code related issues
Active Assembly code adds some div tags around page, slot, snippet and fields. In some cases the previews of pages render properly but AA fails.
Some guide lines to follow.
a) Local templates that do not use global templates must use start and end AA page macros at appropriate places.
b) Custom slot rendering in side templates must use start and end AA slot macros properly.
c) Try not to wrap the snippet template content in td element as this leads to code like <tr>AA Div tags<td>…, causing the page failure.
d) Keep the pages xhtml compliant

Some issues I resolved through tech support calls.
a) One client had same slot call twice on the page by mistake, This caused two elements with the same id and AA page rendering failed.
b). Another client had a slot macro with slot name spelled with different case.