There is a bug in WordPress associated with unwanted breaks (<br />) being created after shortcode expansion which causes formatting problems. This post attempts to document a number of possible workarounds.

The bug is documented at http://core.trac.wordpress.org/ticket/14050

The current WordPress documentation for shortcodes says this bug was fixed in WordPress 2.5.1 (we’re now at version 3.0.5).

Here is the relevant text

wpautop recognizes shortcode syntax and will attempt not to wrap p or br tags around shortcodes that stand alone on a line by themselves.  Note: in WordPress 2.5.0, shortcodes were parsed before post formatting was applied, so the shortcode output HTML was sometimes wrapped in p or br tags. This was incorrect behaviour that has been fixed in 2.5.1.

The problem is particularly annoying to me, as I spent a couple of hours trying to work out where the extra <br />’s were coming from in my most recent post  prior to this one ( Summary of plugins in a WoW website )

Expected behaviour

Two shortcodes on the same line remain on the same line.
Here we can see [ WoW] and [ oik] on the same line
Here we can see WoW and oik  on the same line

Wrong behaviour

Two shortcodes on separate lines with an unwanted break
[ WoW]
[ oik]
WoW
oik

OK, this doesn’t look too bad, but in the previous post the shortcodes were formatted as table rows but all the breaks appeared before the table so there was a big vertical gap. Here, let me show you with [ bw_plug name="oik" table="y"] thrice.

Workaround 1A

Put the shortcodes side by side: [ WoW][ oik]
Put the shortcodes side by side: WoWoik

Workaround 1B

All on the same line but with spaces between them as required: [ WoW] [ oik]
All on the same line but with spaces between them as required: WoW oik

Ineffective Workaround 2

If you want to write them on separate lines for ease of reading
WoW
oik
trying leading spaces DOESN’T work.

Ineffective Workaround 3

Trying trailing required spaces doesn’t work either
WoW 
oik

The real solution

Either implement the fix provided by the person who found the problem. Thanks aaroncampbell

Or use the wpautop-control plugin to choose on a post by post basis whether or not you want automatic paragraphs and breaks.