The most common cause of poor template formatting is creating templates by copying data out of another source (Microsoft Word document, website, an old email, etc...). When you copy data from one source and paste it into your template, a lot of hidden formatting can carried along with it that you didn't intend to include. This formatting might not be expressed inside Gmail but can be expressed in different email clients causing strange or unexpected formatting of the email.
If you do need to copy data out of another source in order to create your template, we strongly recommend first passing it through a plain-text editor. Copy your text and then paste it into the plain-text editor to strip out all the formatting. Then, copy it out of the plain-text editor and paste it into your template.
Notepad is a great plain-text editor that comes with PCs. For Mac, we recommend TextWrangler.