After reading the bug report forums, I decided to make this small bug fix mod.  From the readme;

Install for Entrenchment- Place VarekRaith's Bugfix Mod Entrenchment in your UserName/AppData/Local/Ironclad Games/Sins of a Solar Empire/Mods-Entrenchment v1.03 Folder
Install for Vanilla -  Place VarekRaith's Bugfix Mod Vanilla in your UserName/AppData/Local/Ironclad Games/Sins of a Solar Empire/Mods-v1.17 Folder.

Thanks to Pawelo and ovi-187 for reporting these bugs on the Sins forum!
Additional thanks to Aaron Hall at Malfador Machinations for the file format you see before you.

Version 1.00 September 08, 2009
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1.  Note  - Initial Release.
2.  Fixed - Kortul Disruptive Strikes ability now works properly on its beam weapons.
3.  Fixed - Sova Embargo ability levels 2 and 3 now target trade ships as intended.
4.  Fixed - Vasari Phasic Trap ability now has only one research level.  Erroneously had 2.  Entrenchment only.
5.  Fixed - Dunov EMP Blast now plays correct sound file.
6.  Fixed - Skirantra Nano Repair Cloud now plays correct sound file.
7.  Fixed - Serevun Reactive Nanite Armor now plays correct sound file.

If there are any other bug fixes you'd like that can be modded in, let me know.

http://www.filefront.com/14492707/Varek%20Raith%27s%20Bugfix%20Mod%20Vanilla+Entrenchment.zip

Edit - D'oh! Link fixed.