Few days ago I received an email from the associate editor. He apologized for my paper has mistakenly been left outside of the normal review process. This happened almost 14 months after my submission. I asked the journal editor for information on the status of the review process about 7 months ago and received an email from the technical staff that my status is "in review" as can be seen in Editorial Manager system. The journal is highly ranked and the review process usually takes a long time. So, I thought everything was ok. The associate editor is asking me now if I still want to proceed this submission. Should I say yes?
Unfortunately, these things happen, and it sounds like the journal is at least being appropriately apologetic.
If you go do a different journal, you'll be starting all over again. If this is a good journal for your field, and you think it's an honest mistake, then I would instead recommend asking for an expedited review process. Since the editors are acknowledging they messed things up, you are likely to get faster and better consideration from them than another equivalent peer journal.
So: be collegial and gracious about their mistake, and next time you'll have good reason for when you send an earlier status query.
Many years ago, a colleague and I sent out a paper for publication. My colleague did the actual work of submission. Six months later, he told me he had not received an acknowledgement of receipt from the journal. For this reason, he wondered if he had actually submitted the paper, or whether he had just prepared the submission, but forgotten to mail it.
So I said I would handle it. I resubmitted the paper to the same journal, explaining in a very honest cover letter how we weren't sure if we had submitted it already.
About a week or two later, my colleague received a reply from the journal telling him that the paper had been rejected. Not only had it been rejected, but it hadn't even been sent out for review because the paper was in a subject in which the journal didn't publish.
Now the punchline:
A couple of days later, I received a glowing acceptance letter! And it was obvious from the detailed comments in the report that the reviewer had read the paper very carefully!
Even though this story sounds like an urban legend, this really happened to me! You just don't know what will transpire! Go ahead and give the journal another chance. Maybe they will give you special treatment.
Mistakes happen, no system is perfect, and if nobody is seriously damaged (physically, professionally or in some other way of importance), it is in our interest to allow them, so that we can claim such an allowance for our mistakes, when their time comes, (I apologize for the apparent cynicism, but I am an economist)... let alone of it being the peaceful thing to do.
But this does not mean that the entity that makes the mistake is free to not do anything about it, apart from apologizing. The apology may be sincere, but I would accept it as effective, if it has been accompanied by something along the lines of
"It goes without saying that, if you still want to move on with this submission, we will make every effort to expedite it as much as possible, without compromising the quality of the review process"
...which would mean, contacting reviewers, persuade them to shift priorities, explain why, etc. One should go some distance in correcting/mitigating the effects of, one's own mistakes.