Can I re-enter Thailand after a recent three-month stay on a tourist visa without issues?

The o it issue is that you are Indian. Immigration is concerned about Indian tourist behavior.

There's no new rules. What they are doing is looking at how long each person is staying in Thailand with visa exempts and extensions that indicates they are trying to live there for months without a visa. You've entered 2 months without a visa plus a one month extension, then went back to your home country? It should be ok but there are never any guarantees. Make sure you fill in the TDAC, have evidence of accomodation booking and 20k baht cash in any currency. There are agents that check your travel history and offer assistance for smooth entry.

Based on what you’ve written, there is no real issue at all. You have only spent about three months total in Thailand in your entire life, which is well within normal tourist use. Under the current practice, that does not raise any red flags. If you return now, you should normally be granted entry again on visa exemption, provided you have an onward or return ticket within 60 days, accommodation details, and funds if asked. The so-called “new rules” are aimed at repeated back-to-back stays and long-term use of visa exemption, not at cases like yours. You do not need an agent or any special assistance for this travel history.