Well, Malay and Indonesian share the same words, most with similar meanings with some with vastly different meanings and used in different context. Eg hospital in Malay is just hospital, but in Indonesian it is rumah sakit (literally sick house), also punggung in Indonesian means shoulders, in Malay it means the butt. Usually we understand each other though. Hope it helps!

it's pretty lot different between Malaysian and Indonesian. Although both have same word, but actually bit different in meaning and its uses in context. Even sometimes I can't understand some Malaysian.

Yes, there are lot of differences between Malaysian and Indonesian...