Student or Learner
Diferences between each other, In spanish they have the same meaning but in english has a tricky usage
on / in / at
sobre la mesa/en el mundo/a la una
I think what you mean is that your bilingual dictionary gives them as synonymous in certain contexts. The contexts for 'on/in/at' are not the same as the ones for sobre/en/a; something can be on or in time, but not at - whereas you can say en tiempo and a tiempo*, but not sobre tiempo and not a un tiempo (to match English 'at a time'); you can say sobre la mesa, en la mesa, and a la mesa - but in English you can only say 'in the table' if you mean 'in the <Noun> of the table' ('in the drawer of the table [assuming that the table has one]' or '[hidden] in the fabric of the table'). In each language the distribution of those (and other) words to go with possible contexts is different. You can very seldom say 'this word = esta palabra, but bilingual dictionaries encourage you to think you can, and to believe that learning another language is just a matter of learning a few equivalences.
If you don't have a good monolingual dictionary, get one; and use your bilingual one with great care. End of lecture. ;-
*Not, of course, with the same meaning; I'm just talking about possible collocations.