"The water is in a glass."
Translation:Το νερό είναι μέσα σε ένα ποτήρι.
If the full, correct translation of "in" in this case is μέσα σε, then the dictionary hints ought to show that.
Also, it would be helpful if the Notes & Tips section would mention the many uses of από and of σε, especially as combined with other prepositions. The current list of prepositions is actually a little misleading.