The symptoms pictured (mainly the leaf blister-like bumps) look like edema. This is caused by over-watering, or the inability of the plant to dispel extra water in its tissues when the atmosphere is too humid and the roots too damp. Cell damage from excess water is what causes the scarring. While this cannot be healed, any new growth should not develop symptoms if the issue is resolved. To avoid root damage from over-watering, make sure the pot needs watering rather than watering on a schedule or without checking the soil first -- citrus need to dry out a bit between waterings, more so than most other houseplants. Feel the soil at least an inch or two deep into the container (how much depends on container size and how moisture-retentive the potting mix is): it should feel fairly dry to the touch at that depth before watering is needed. Similarly, if the pot sits on a saucer, make sure the saucer is emptied promptly after watering so any collected water doesn't seep back into the pot, which will effectively suffocate the lower roots. Root stress and dieback is one potential cause of yellowing leaves.

Other causes of leaf yellowing can include the scale insects you mentioned, plus malnourishment. Insufficient nitrogen (N) can cause lower leaf yellowing, as can insufficient light. (In a greenhouse, unless it's heavily shaded, light level is probably not an issue.) Citrus can benefit from a bit more iron (Fe) content in their fertilizer compared to other houseplants (and not all fertilizer formulations even contain iron), and they also grow best in an acidic soil (in the pH range of 5.5 to 6.5). These factors go hand-in-hand, since soil that isn't acidic enough won't allow the roots to absorb what they need, even if iron in the soil is plentiful. Although the results can sometimes be hard to interpret, a home pH test kit might suffice if you are concerned that the potting mix isn't acidic enough. While laboratory soil testing is the best way to measure pH in outdoor soil, with used on potting mix for container-grown plants, the test won't be accurate.

Other environmental stressors can contribute to leaf yellowing and shedding, like cold drafts, heat stress, air pollutants from heaters that aren't burning fuel cleanly, and phytotoxicity (injury from chemical exposure, which can include pesticides). If you're following the label directions on the neem oil, using the right concentration (if you're diluting it from concentrate) and interval for spraying, then that's probably not a factor here.

For now, you probably just need to focus on avoiding overwatering as the most likely issue resulting in leaf damage, and the plant can go back outside for the summer once temperatures moderate in late spring. If useful, our Growing Dwarf Citrus page provides general cultivation tips.

Miri