Where / how did you save the HTML file to Alfresco? Are you talking about the editor in the Wiki / Blog site components? When storing an HTML file in the document library or repository, Alfresco does NOT remove script tags, but if you are using a richtext editor UI (i.e. in Inline Edit, or the wiki / blog components), then Alfresco will strip out potentially harmful HTML content, including script tags. There is a (very old) blog post about the HTML black/whitelist processing that may help if you really think script-tags should be kept (generally, they should not).