The first and biggest reason is lazy pronunciation and slang. Native speakers of a language tend to be much less precise in the way they say and even use words often without noticing that they are doing it.
Have a look at this video of a British man talking about just this with his dialect of English.
This also brings us to the second main reason words may not sound they way you learned them: regional dialects. Gaelic has lots of them. Some times they say the same word differently from the way you learned, sometimes they may even use a different word.
Here is a great set of maps to help show some of these dialectical differences
Scottish Gaelic Dialect Survey
Another good way of getting a handle on dialect differences is to hear them. Listen to BBC Radio Nan Gaidheal, look at some of the videos on e-Stòras and Guthan nan Eilean check out some you tube videos ( try putting Nova Scotia Gaelic in the search box) and keep looking around on-line as there is new stuff all the time.