Recently submitted a manuscript which got a decision of Reject & Resubmit, i.e. the editor invited a resubmission provided we can address the reviewer's comments. In my previous experience, all my manuscripts were always accepted after a resubmission was invited, so I thought the editors basically use this type of decision to give themselves a little more leverage.
One reviewer's comments were very negative, but unjustifiably so. For example, he/she stated that the "experimental treatments" weren't independent, while our study was purely observational and didn't include any experimental manipulation. The comments looked like they were made by someone who didn't bother to put any thought into the review and had a poor understanding of statistics (our study is loosely in the field of ecology/conservation).
We rebutted these comments firmly, but politely. The other comments, including those made by the second reviewers, were minor and were addressed by revising or clarifying the text in certain places.
We also explicitly drew attention to the issue with one reviewer's comments in the cover letter accompanying the resubmission. We stated that we carefully considered these comments, but they were unjustified, and again explained why.
This resubmission was rejected outright very quickly, within a week. The editor acknowledged the revision did improve the manuscript, but still rejected citing the standard "our acceptance threshold is very high" etc.
It is the first time my invited resubmission was rejected, and I can't help wondering whether the firm response to the reviewer's comments was the cause.