Numbered ordering of multiple citations

This functionality is provided by the cite package. By default it will also compress lists of citations so [1,2,3] becomes [1-3], however a document stating with

\documentclass{article}

\usepackage[nocompress]{cite}
\bibliographystyle{ieeetr}

will produce the effect you wish. Sorting can be turned off by using the [nosort] option.

Incidentally, I notice that there are alternative bibliography styles for IEEE Transactions, called ieeetrans which include a variant ieeetranS that sorts citations by default. These styles seem to be newer. May be you should consider using those instead.