There are a couple of things I see, but the most important is that there's nothing in the rest of your labs to indicate hyperthyroidism...
Your Free T4 and Free T3, actually, indicate hypothyroidism. Your Free T4 is only at 22% of range and most of us feel best when Free T4 is about mid range. Your Free T3 is at 46% of range and most of us feel best with Free T3 in the upper half to upper third of its range.
Even though you may have Hashimoto's, it also appears that you may have Secondary or Central hypothyroidism, as your main problem. Secondary hypothyroidism is when the pituitary gland doesn't produce enough TSH to stimulate the thyroid to produce enough thyroid hormones. This would be a pituitary problem, at this point, not a thyroid problem; though with Hashimoto's, it would eventually become a thyroid problem.
What, if any, symptoms do you have?
Thyroglobulin Antibodies (TgAb) is a marker for Hashimoto's, as is Thyroid Peroxidase Antibodies (TPOab).
Since your TSI wasn't elevated, it sounds like you could be having a hyper phase of Hashimoto's - if you're hyper, that is. Is TSH the only thing that was tested to determine thyroid function? What about Free T4 and Free T3? If they were tested, please post the results, with corresponding reference ranges. Just because they were "in range" doesn't mean they were adequate.
Nodules are very common with Hashimoto's and are usually nothing to be concerned about, but your endo may suggest an FNA just to sure, since your largest is greater than 1 cm and solid.
Excerpt from the book "Why Do I Still Have Thyroid Symptoms When My Lab Tests Are Normal?" by Dr Kharrazian...
"Hashimoto's Disease and "Normal" Lab Results
Jan - TSH 4.5
Feb - TSH 0.08
Mar - TSH 2.3
April - TSH 3.8
May - TSH 8.7
June - TSH 7.4
July - TSH 1.6
One reason hypothyroidism goes misdiagnosed is because a person with Hashimoto's can present with normal TSH. This graph illustrates the monthy TSH levels of a person with Hashimoto's who is receiving no treatment. As the autoimmune condition fluctuates, TSH levels vary wildly. Using standard lab range of 0.45 - 4.5 this person would fail to be diagnosed. During the month of March the patient's TSH even falls within functional range 1.8 - 3.0. That's why also testing for immune antibodies and evaluating symptoms and history are so vital."