Surprisingly Agilent only claim 10% size accuracy above 300 bases ( user manual p 15 which is not vey good and the size standards are getting quite close together above 500 so I would call Agilent tech support to discuss a different algorithm for curve fitting of the standards and to ask what factors are relevant in incorrect sizing. Do the large bands correspond to samples with heterozygous changes in which case possibly the large peak is a heteroduplex which can be very large in non denaturing conditions

I am not an expert specifically on Agilent Tapestation 2200, but I have seen similar issues in Sanger sequencing after PCR amplification of specific loci. PCR bands often show the most common products of a PCR reaction, although longer products do accumulate during the amplification process which might not be visible on agarose gel with EthBr staining due to insufficiency of the products. This problem most commonly arises due to longer annealing and amplification times in thermalcycling, and using more than required amounts of template DNA in PCR. Say forward primer binds to one strand and reverse to the complementary strand on original template sequence. DNA Polymerase, by no means, has any restriction to stop amplifying DNA exactly on the binding site of the other primer on template DNA, and keeps on adding more nucleotide until the reaction is stopped by denaturation step. In next cycles too, same process happens on original template strands. If your primers are not annealing to non-specific sites, then perhaps you may proceed with Sanger sequencing of a couple of amplified products, and trim the extra length sequences (which will be of poor quality obviously). To get rid of this problem, optimize your PCR reaction with minimal amount of template DNA (by making serial dilutions of template DNA), and keeping annealing and extension times to lower possible ends. Hope this helps.

Fundamentally, results of an (properly conducted) experiment are never "wrong". They may not agree with your expectations, but then the problem is with the expectations, not with the result. Science is about falsification (see Popper 1935, https://monoskop.org/images/e/ec/Popper_Karl_Logik_der_Forschung.pdf), so always keep an open mind for what nature is telling you!