Never Heard Back on PhD Application but enrolled in MS program Applied to a private university for admission to an MS program thinking I had no chance being admitted to the PhD program because of my transcript.
Planned on trying to get into the PhD program after the first semester of the masters program. At a welcoming seminar for new grad students a faculty member told me to apply to the PhD program anyway. So I did, back in November for Spring admission. Still have not received a formal decision on the PhD application and it’s the end of the Spring semester. Tried reaching out to faculty multiple times inquiring whether I should reapply etc. have not heard back regarding the PhD application but have on other things like maybe an independent research study over the summer. One of my professors straight up told me sometimes the admission committee purposely does not make a decision on certain applicants because they’re not sure about them yet. Which is fine and understandable in a way. But it’s pretty ridiculous at this point, like I’m enrolled in the MS program, have corresponded with multiple faculty regarding research projects etc. but no decision on my PhD application? What should I do?
I’ve respectfully inquired a couple of times but after sending 1-2 follow up emails I don’t feel comfortable continuing to try because I don’t want to come off as rude but this is very important to my future. The chair even got back to me but only addressed half my email and said nothing of the PhD application. I’m not dumb, I know this could be code for declined, but why not give me a formal response?? If anyone wants to know any other details before giving input just ask. Thanks.
I sympathize with your situation. To help understand your situation better can you indicate whether it is a US university and if you are an international or domestic applicant? Thanks.  Regardless, please see my response below, which is assuming you are an international student applying to a US private university.
There is a fundamental difference between Ph.D. and MS hires. Most international Ph.D. hires are paid (albeit menially) a stipend and their tuition is covered via research / teaching assistantships. In contrast, MS students bear their own tuition costs and in fact are a source of revenue for university departments. Therefore, money is potentially one reason that is causing this delay from their side.
Another delay is simply due to Ph.D. hiring cycles.  Most professors are part of committees they'd rather not be.  Ph.D. hiring is another such committee.  Therefore, many departments have fixed cycles within which they would proceed with the hiring.  Perhaps, you are ahead of the cycle in your department.  You can check this by asking pointed questions.
Additionally, professors in the US have the power to hire Ph.D.s at will if they have money.  Your discussion with a professor is a good way to ensure that your application is given priority.  However, remember that when a professor hires a Ph.D. student, they begin a long journey (5 years on average) during which a strong working relationship will be established between the two of you. Essentially, they are investing in you.  So keep that in mind in your conversations with the professor.  Furthermore, sometimes talking to current Ph.D. students who are already working in that group is a good way to figure out crucial information about the professor such as &quot;do they have money/funds to support another Ph.D.?  What is their nature and their expectation from the incoming student?  How helpful are they with job searching / student placement later? etc. &quot;
You mentioned an individual research project with a professor.  While it is useful to do this as it indicates to you whether you enjoy research, enjoy working with the professor and lab, it can also be a waste of time if you already know you want to get in the Ph.D. program with that professor.  Regardless, if nothin else works, an individual study is a great way to build a relationship and show your talent.
Lastly, I want to talk a little about approach.  Most students, especially those starting out, will likely be shy of asking the direct (and at times tough) questions.  It is important you mindfully not be shy/apprehensive.  However, also try not to come off as rude/impatient.  Communicating via email is an art that is learned overtime.  However, below are some pointers that may help:

Write short emails with pointed questions
Always try to be pleasant, try to not sound irritated, especially on email
If an email cannot be made short enough to be read in 1 min max., request the professor for an appointment. Indicate that a brief meeting of 15 mins will be enough, and get the conversation going
Use departmental resources such as graduate coordinator staff, other Ph.D. students to get a good idea on relevant background matters

I am pretty sure they are not being non-responsive because they think you are not qualified.  If it were that clear, they would have told you that.  I rather think that there is some kind of miscommunication / misalignment going on.  I hope it is sorted out for you soon.
Best luck!