1. Take the Bus, Train, Plane...
This is a very common mistake to make because it is a very tempting one. In English, you "take" the bus, the train, the plane ... In Japanese, however, you do NOT say 電車を取る (densha wo toru). Unless, of course, you are Godzilla and you are grabbing one of the trains in your big hand or you are a kid holding a train toy.
In Japanese, you have to use the verb 乗る (noru) and be careful that we use the preposition に (ni) before this verb: 電車に乗る (densha ni noru).
Same for the bus, plane, etc...
2. Take a Shower, Take a Bath
Again, unless you are Godzilla... the verb "toru" won't work here. Use シャワーを浴びる (shawa wo abiru) or お風呂に入る (o furo ni hairu // can be understood as "going in the bath").
While, we are in the bath vocabulary, another common issue is to refer to the water of the bath as 水 (mizu). For example, when you say that there is not enough "water" in this bath, or that the "water" is too warm or too cold. In Japanese, you have to use the word お湯 (o yu // hot water). It won't really make sense to Japanese people otherwise.
3. Take a Medicine
This one is kind of hard. Even today, it doesn't feel very natural for me to say it. In Japanese, we don't "take" a medicine, we "drink" it, even if it isn't a liquid: 薬を飲む (kusuri wo nomu).
So, here is a dangerous confusion. If a Japanese friend tells you この薬取って (kono kusuri totte), it means "bring me this medicine", NOT "take it" (basically, "take it to me").
4. Take an Exam
Another quite common use of the verb "to take" in English is when referring to tests, exams, etc... In Japanese, again , it wouldn't make any sense to use the verb "toru" in this case, and they have the specific verb 受ける (ukeru).
That's it for today! There are other cases where "take" is not translated into "toru" but they are less common (take a nap, take bets, take the bull by the horns...). Remember the four mentioned and you should be fine most of the time :)