The first I am sure is with InfoPath 2007 beta 2 only, and hopefully is an oversight on Microsoft's part that will get fixed.
When submitting a filename to SharePoint 2003 that contains a comma, it is converted to an underscore and saved, while other punctuation marks remain unchanged. To get around this, you must programmatically submit your file with your custom filename.
The other bug just recently revealed itself, and I've seen it in InfoPath 2003 as well. When opening the script editor to edit in JScript, there are duplicate toolbars with no buttons in them, for example, I have 2 Debug, 2 Debug Location, 2 Design, 2 Formatting, etc., except for the Build, Fullscreen, and Menu Bar Toolbars. I can't hide either of the 2 Refresh toolbars, and I can't delete any toolbars from the customize toolbar window.