Difference between Special Issues and Regular Issues

The different journal may put different meaning into "special issue" It could mean that papers have been invited around a certain theme, it could mean papers come from a workshop or symposia, or that the journal has decided to gather papers around a specific topic for some reason. The point is that a special issue differs from a regular issue in that the papers constitute a collection around a theme or coming from a specific group of authors or events. Such issues can either be a decision by the journal or a request from a group of scientists to publish around "their" proposed theme. There may be additional cases but these are the ones I am familiar with within my field.

the best papers at a particular conference often get invited to a special issue of a journal. The editor of the special issue is typically one of the conference chairs, but the papers still go through the regular peer-review process of the journal and are held to the same standards.

In addition to publishing selected papers in conferences (as mentioned by @Mangara), a publisher can announce a special issue journal to concentrate on a particular set of fields which may be a subset of its overall scope.
One main point to note is that special issues have an added advantage that they are time-bound. That is the dates for the first review result, acceptance/rejection, and publication, are all scheduled. Although sometimes, the dates may be subjected to change, this is in contrast to regular journals where the time-frame may not always be estimated.
It can vary. I have seen special issues for (1) conference, (2) theme, (3) some famous professors' birthday/retirement.
In general, it really doesn't matter in terms of citations, just do a full cite including issue number and the like. Nobody will notice/care about if it was special or normal. It will still get cited, abstracted, held by libraries the same way.

Regular issue is what is published monthly or a quarter as per the schedule of the journal publication. Special Issue is for special events like conferences, seminars or some theme.