The larger band might be due to introns or alternative splicing events in the mRNA, which were not anticipated. To address this, verify the genomic structure of your transfected gene for unexpected introns and perform RT-PCR using primers spanning exon-exon junctions.

Another possibility is plasmid backbone contamination, where residual plasmid DNA in your transfected cells includes sequences outside your target gene. Treat your RNA samples with DNase before reverse transcription and confirm the absence of plasmid DNA with a control PCR without reverse transcription.

Primer design issues could also cause this problem, as primers might anneal to unintended sites. Recheck primer specificity using a tool like Primer-BLAST. Non-specific amplification or primer-dimer formations can sometimes produce unexpected bands, so optimize PCR conditions such as annealing temperature, magnesium concentration, and cycle number, possibly using a gradient PCR.

Cell line-specific effects might alter the size of the mRNA transcript if the plasmid integrates in unexpected ways.

Ensure all experimental controls are correctly set up, including a non-transfected cell line, a no-template control for PCR, and a housekeeping gene for RT-PCR.

Yes this is normal. Higher loading amount causes faster migration. I think the mechanism of this is physical destruction of the gel by earlier molecules, which creates channels through which later molecules can then follow with less resistance. That's also why the ladder's ability to measure size is generally limited. Gel migration is only quantitatively comparable when you have low amounts of a similar molecule loaded from the same matrix.

To cut a long story short, I think your experiment worked just fine.

You have very overloaded wells in the control!!!! To begin with, apply the same amount of DNA (approximately) to the control and test samples, because overloaded wells may lead to incorrect conclusions.