"That is just a general rule."
Translation:Tio simple estas ĝenerala regulo.
I think you mean "which look as if they have an affix in them"?
Oh yes, tons.
A kolego (colleague) is not a big neck (kol-eg-o), a putino (prostitute) may be female but she is still no female well (put-in-o), a miliono (million) is not a fraction of milletgrass (mili-on-o), nor is a kanono (cannon or canon) a fraction of a cane (kan-on-o). Sugar (sukero) might be present in drops of juice (suk-er-o) but that's not where the name comes from. Aĉeti (to buy) is not the same as being a little bit horrid (aĉ-et-i). And so on and so on.
That's what a good Esperanto dictionary will show which part of a word is the stem; any letters that look as if they might be suffixes but come before the end of the stem are not suffixes.
For example, PIV shows regulo (rule) as "regul/o", indicating that "regul-" is the stem and that it does not contain an affix -ul-.
You can also get homophony by how you split up a word into prefix(es), suffix(es), and stem(s), e.g. revido could be either re-vid-o "seeing again" or rev-id-o "dream-child".
And to answer your half-spoken question: "regulo" could also mean "person who rules" (reg-ul-o).
Oh, and you also have another class of nouns which look as if they are compound nouns, but they aren't.
For example, "steko" is a steak and "rumsteko" is a rump steak - but "rumsteko" is listed as "rumstek/o" so its stem is rumstek-, which means that it is not composed of rum- + stek- + -o, even though it looks as if it could be.
Or "televido" is tele- + vid- + -o, but "teleskopo" is teleskop- + -o.
Or "geologio" which is geologi- + -o but "bakteriologio" which is bakteri- + -ologi- + -o.
It's not always consistent.
The classical monolingual dictionary of Esperanto is the Plena Ilustrita Vortaro (PIV); it's available for online at http://vortaro.net . Use is free for registered users. If you have a lernu.net account, that works for vortaro.net as well.
Stems are indicated either by a stroke "/" or a superscript number (e.g. "³") at the end of the stem and before the ending. (The number indicates that the word was added to the official Esperanto dictionary, the Universala Vortaro, in a later addendum. There have been nine such official additions, the last in 2007 (words from this one may not be in the online PIV yet since I think it's based on the 2005 printed edition).
Stems are only indicated for the base word of a given entry; any sub-entries of this will be assumed to have the same stem. What other stems are on those sub-entries one will have to guess, but since they are usually just prefix+stem, stem+suffix, or stem+stem, it's usually not ambiguous.