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Can you include a photo? This could be an invading weed that has flowered while growing up a tree. This would be uncommon for this to occur. If you can include a photo, then I will be better able to help you.

It sounds like your tree may have a nutrient deficiency. Pale green leaves can be a sign of lack of nitrogen or of lack of micronutrients, and lack of flowers can indicate a phosphorus deficiency. I recommend applying a balanced NPK fertilizer ase described in this article:
http://extension.uga.edu/publications/detail.cfm?number=C974

Organic options like compost or bone meal (provides phosphorus) are also available. Magnolias also prefer slightly acidic soil (pH 5.5-6.5), and this will help them absorb nutrients better.

Alternatively, if the magnolia is growing in dense shade, lack of light may cause these symptoms. Partial shade is fine.

They are, usually, self cleaning, and the flower will yield to fruiting cones. There will be no need to interfere with their natural process.

I would amend the soil with some organic soil amendments, such as compost.
These articles will help you.

https://www.gardeningknowhow.com/ornamental/trees/magnolia/magnolia-blooming-problems.htm
https://www.gardeningknowhow.com/special/organic/the-importance-of-soil-for-an-organic-garden.htm
https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/how-to-improve-clay-soil.htm

Check the stems; do they bend or snap off and break?
Magnolias are tolerant of a wide range of soils, including average soils and dry soils. The ideal soil is rich, acidic and porous, with a pH between 5.0 and 6.5. To make soil more hospitable before planting, mix in leaf mold. Be sure to plant your "Jane" magnolia in its final location, as magnolias have large, complicated root systems that have trouble recovering if dug up and transplanted. Mulch well to help retain moisture in the soil; the "Jane" magnolia needs average amounts of water.
Once the rootball is covered with quality dirt -- as the trees do not do well in constricting clay -- water the soil thoroughly. Do not be afraid to overwater at planting, as this will help the roots establish. But avoid keeping the tree in saturated soil. While magnolias do well in areas where moisture applications range in extremes from too dry to too wet, any plant's roots can drown if it's constantly kept in water. Allow the soil to dry out slightly between applications as the tree establishes.
https://www.gardeningknowhow.com/ornamental/trees/tgen/tree-scratch-test.htm
https://www.gardeningknowhow.com/ornamental/trees/tgen/sudden-tree-death-causes.htm

Yes, this does appear to be a fungal infection from remaining in over-wet soil for too long. If your area is prone to heavy rainfall, then I would recommend removing the mulch until it dries out some.

You can attempt to correct this using wettable sulfur and dolomitic lime. This will kill off any infection that is able to be killed, while reconditioning the soil back to a more suitable condition for the tree.

Make sure to only water if the soil is completely dry. These are fairly drought tolerant, and will prefer to dry out between waterings if possible.