It doesn't conform to the usual style for academic paper titles in English, which is that the title usually functions as a noun phrase describing the paper's content. Your "Study the..." title seems to instead be a verb phrase describing what the author did, or maybe what the thesis is going to do. It also happens to function as a complete sentence with "study" in the imperative mood, which as others mentioned, makes it sound like a command.
Adding "of" helps, in that it makes "study" function instead as a noun (meaning "examination", "investigation", etc), and so it sounds more like a noun phrase.
Personally, I would remove "study" altogether as it's redundant: the reader already knows that the paper is studying something, that's the whole point of a thesis. So I'd just make it "Phase-shifting behavior in the complex reaction mechanism".
I'd also look carefully at the definite article "the" before "complex reaction mechanism". If this is a term of art in your field that refers to a specific mechanism, and when you say "the complex reaction mechanism" people know exactly which mechanism you mean, then "the" might be okay. But if you are simply talking about an unspecified reaction mechanism that happens to be complex, then you would not use a definite article, and would instead say something like "Phase-shifting behavior in a complex reaction mechanism", or "Phase-shifting behavior in complex reaction mechanisms." Articles ("a", "an", "the") are often a challenge for learners of English, so you might want to consult with someone who knows the terminology of your field, and is experienced with reading and writing academic English.
If I were in your situation, I would make a reasonable effort to get the title changed. If it's a matter of filling out a form, or making a phone call, or contacting the boss of whoever told you that you couldn't do it, it would be worthwhile. Even if it's a university rule, there is almost certainly some person or group who has the power to make an exception, and there is also very likely to be a process for making a formal request to that person or group. On the other hand, if it would require a major hardship to get it changed, like paying a large fee or delaying graduation, then I would just let it go.
Relatively few people are likely to read your thesis anyway, so it probably isn't such a big deal. But if you will be publishing one or more papers based on your thesis, they will be more visible, so you'll want to be more careful with your grammar and proofreading.
Also, when listing the thesis title on your website, CV, etc, I would be inclined to list the corrected title. Yes, yes, normally you should always cite documents by their exact title with no changes, but adding a stop word like "of" isn't really going to cause any problems.