1) pre tags - being that pre tags take into account formatting, removing whitespace is going to alter how the content is rendered
2) any empty tags - its becoming a thing of the past but there are many instances where browsers will render a tag with a single space inside differently than a tag with nothing inside. In other words, space within a tag may be intentional by the developer.
3) spaces inside attributes may matter - you could have an attribute on an html tag that say is data-whatever="1 2\n 3" and potentially reducing those spaces could be bad - depends upon what the developer intended
Additionally there are some other things to consider...
1) GZIP if used will make the impact of scrubbing out whitespace almost nonexistent
2) Most HTML served is dynamic, meaning that the HTML compression will need to be run on every HTML response - this could have some performance negatives. (If your just compressing static HTML once it should be fine.)