To start with a quote (from Wikibook):
If a friend of yours wants to give you his/her template, it is a very nice gesture. Say Thanks, but no, Thanks. You won't believe how many strange stuff is in there without him/her even noticing it. All those are little tripwires that you don't want in your document. Unfortunately, the same is true for many templates you can find online.
The following text summarizes some common points. (In the following text the term "template" is meant for every piece of code you'll find out there providing a full-featured TeX document which just misses the content and, of course, those custom document classes you'll find everywhere.)
Many templates you'll find are built on the command set of LaTeX 2.09. That includes commands like
\bf etc. which should not be used in recent documents. Those old commands may cause some harm especially working with some document classes (see, e.g., KOMA) you may want to use.
Many templates have crashingly bad code, often from using packages and classes that are incompatible with one another. (
classicthesis is a prime example.)
above sentence taken from a comment by Alan Munn
In addition some problems with maintenance may occur as there are templates that were published once, but are not maintained anymore. If you encounter bugs (bugs are not not modification requests) in such a template, you may have to solve them on your own.
Another problem with templates is that you will find many templates made on purpose. So a thesis template for university X probably meets the style requirements of university X, but not Y. You should not even try to use it at Y, because most templates do not want you to modify them.
Overload of packages
Many templates also tend to load a whole bunch of packages. Some of them aren't even needed and some of them may clash with packages you need to use. You could try to rewrite or delete parts of the template, but that's cumbersome.
Predefined structure and dependencies
Some templates (especially for bigger projects) also force you to use a specific file and folder layout, because they link to an image file or a file in another directory. Sometimes templates even include a reference to a package which is not distributed with all distributions, but only some (or has to be downloaded).
It's getting even worse if the name of the template clashes with other packages (or if it's too general like
Problems in typography
As in every other subject you should understand what you're doing. Some templates change typographic conventions and want to force you to some specific style. That's especially problematic as typography differs around the world. American style is not always applicable in Germany, for example.
Mostly it's better if you learn how to present your data (which is also important) in the traditions of your country's typography (look, e.g., at
Do not use a (complex) template if you do not have to. If you're studying at a university forcing you to use a specific template, you should use it, but if you're free to choose your style, just start off with a very basic document and spend some time learning LaTeX to get the style you want without using a complex template which does not suit exactly your needs.