Well, I know little about your issue, therefore, I made a little survey on the web and found some interesting information for you. In this paper, they mentioned that recent studies suggest that American alligator blood is effective in reducing colorectal cancer cell viability in vitro, previous research found that crocodile blood displayed marked effects on cancer cells not only with anti-23 strains of bacteria, including those resistant to antibiotics but also with antioxidant and anti‑inflammatory properties. Yet the mechanism remains unclear.

They explain that the whole blood and fraction preparation. The crocodile blood powder was purchased from a local vendor and dissolved in phosphate‑buffered saline (PBS). After sonification, the mixture was centrifuged at 10,000 x g for 20 min. The supernatant was collected. After precipitation by ammonium sulfate overnight at 4˚C, the mixture was centrifuged at 10,000 x g for 20 min. The supernatant and residues were collected and desalted by Sephadex G25.

It doesn't do like yours (freezing blood ate -20°) but I think it could help.

The work is "Crocodile blood extract induces the apoptosis of lung cancer cells through PTEN activity"

Article Crocodile blood extract induces the apoptosis of lung cancer...

And there is another one that collected approximately 1 ml of blood and it was drawn from the nuchal sinus of each crocodile and immediately decanted into an equal amount of buffer (10 mM Tris, pH 7.6). Samples were initially stored at room temperature and later at −20°C for long-term storage. All individuals were permanently marked for future identification by notching the dorsal edge of a unique series of caudal scutes and then released at the site of capture within 24 h.

The study is "Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize"

Article Integrating molecular, phenotypic and environmental data to ...

And the other one I found that could help you. They collected blood and tissue samples at the beginning of the rainy season in SR (2007) and PV (2005, 2008 and 2009), throughout the year in LB (2007 – 2009), during the rainy season in RT (2005 – 2006) and during the end of the dry season in ACOSA (2006, 2008 and 2009). We captured crocodiles mainly during spotlight surveys using the break-away snare method (Hutton et al. 1987; Hutton and Woodhouse 1989), snake tongs or by hand (see Mauger et al. 2012 for additional information on sample collection). Blood and/or tissue were collected from 184 individuals (see Table 1 for the size class distribution of samples). In sites where a large number of hatchlings were captured, a random number selector was used to randomly select four to six hatchlings for genetic analysis. Tissue was collected from the caudal scutes during marking and blood was collected from the caudal vein or the dorsal sinus. Tissue samples were preserved in 95–100% ethanol. Blood was preserved on Whatman FTA Cards for DNA Preservation® (GE Life Sciences).

The work is "Conservation genetics of American crocodile, Crocodylus acutus, populations in Pacific Costa Rica"

https://doi.org/10.3897/natureconservation.17.9714

Well, you should look again at your sampling method and storage, it's unusual to get some mistakes on the QIAGEN kit, your problem may be on the other processes you did. I hope this information can help you.

You can also try to increase time of Proteinase K treatment