I guess you’ve echoed the result of shortcode callback function rather than returning them. Please check here: http://codex.wordpress.org/Shortcode_API
Shortcodes are written by providing a handler function. Shortcode
handlers are broadly similar to WordPress filters: they accept
parameters (attributes) and return a result (the shortcode output).
you need to return the output that will be added to your content. if you echo them, it will be printed before the content.
if this is the not problem, please put the codes so that we can see what is the error.